diff --git a/.github/workflows/ci-e2e.yml b/.github/workflows/ci-e2e.yml new file mode 100644 index 000000000..b9c11da2b --- /dev/null +++ b/.github/workflows/ci-e2e.yml @@ -0,0 +1,80 @@ +name: Tests + +on: + # always run tests when pushing to main + push: + branches: [ main ] + + # only run tests on pull requests which actually modify files that affect the tests + pull_request: + branches_ignore: [] + # for now, the tests defined in this file are only run when any of the following paths are modified: + paths: + # workflow definitions + - '.tests/**' + + # github workflow configurations + - '.github/**' + + # 'base' files of snappy-pipeline + - 'snappy_pipeline/*' + - 'snappy_pipeline/workflows/abstract/**' + + # steps used in the test workflows + - 'snappy_pipeline/workflows/ngs_mapping/**' + - 'snappy_pipeline/workflows/somatic_variant_calling/**' + - 'snappy_pipeline/workflows/somatic_variant_annotation/**' + - 'snappy_pipeline/workflows/somatic_variant_filtration/**' + + # 'base' files of snappy_wrappers + - 'snappy_wrappers/*' + + # wrappers used in the test workflows + - 'snappy_wrappers/wrappers/alfred/**' + - 'snappy_wrappers/wrappers/bcftools/**' + - 'snappy_wrappers/wrappers/bwa/**' + - 'snappy_wrappers/wrappers/link_in_bam/**' + - 'snappy_wrappers/wrappers/mutect/**' + - 'snappy_wrappers/wrappers/mutect_par/**' + - 'snappy_wrappers/wrappers/mutect2/**' + - 'snappy_wrappers/wrappers/mutect2_par/**' + - 'snappy_wrappers/wrappers/ngs_chew/**' + - 'snappy_wrappers/wrappers/somatic_variant_filtration/**' + - 'snappy_wrappers/wrappers/vep/**' + + +jobs: + + Dryrun_Tests: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + lfs: 'true' + - name: Test workflow (local FASTQs) + uses: snakemake/snakemake-github-action@v1 + with: + directory: .tests/test-workflow + snakefile: .tests/test-workflow/workflow/Snakefile + args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dryrun" + show-disk-usage-on-error: true + + + Tests: + runs-on: ubuntu-latest + needs: + - Dryrun_Tests + steps: + - name: update apt + run: sudo apt-get update + - uses: actions/checkout@v4 + with: + lfs: 'true' + - name: Test workflow (local FASTQs) + uses: snakemake/snakemake-github-action@v1 + with: + directory: .tests/test-workflow + snakefile: .tests/test-workflow/workflow/Snakefile + args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache" + show-disk-usage-on-error: true + diff --git a/.tests/test-workflow/.gitattributes b/.tests/test-workflow/.gitattributes new file mode 100644 index 000000000..e69de29bb diff --git a/.tests/test-workflow/.gitignore b/.tests/test-workflow/.gitignore new file mode 100644 index 000000000..2e299c990 --- /dev/null +++ b/.tests/test-workflow/.gitignore @@ -0,0 +1,8 @@ +**/.snappy_path_cache +**/.*.lock +**/output +**/work +logs +snappy-pipeline +pipelines/*/.snappy_pipeline/config.yaml +**/__pycache__ diff --git a/.tests/test-workflow/config/cancer_wes/config.yaml.jinja2 b/.tests/test-workflow/config/cancer_wes/config.yaml.jinja2 new file mode 100644 index 000000000..815a47826 --- /dev/null +++ b/.tests/test-workflow/config/cancer_wes/config.yaml.jinja2 @@ -0,0 +1,61 @@ +static_data_config: + reference: + path: {{ params["reference"] }} + +step_config: + ngs_mapping: + tools: + dna: [bwa] # Required if DNA analysis; otherwise, leave empty. Example: 'bwa'. + bwa: + path_index: {{ params["bwa_index"] }} + mask_duplicates: false + memory_bam_sort: 2G + num_threads_bam_sort: 2 + num_threads_bam_view: 2 + num_threads_align: 2 + ngs_chew_fingerprint: + enabled: false + target_coverage_report: + path_target_interval_list_mapping: + - name: MedExome_hg19_empirical_targets + pattern: MedExome + path: ../resources/Exome-MedExome.chr12.bed + + + somatic_variant_calling: + tools: [mutect2] + mutect2: + ngs_mapping: ../ngs_mapping + extra_arguments: [] + window_length: 300000000 + keep_tmpdir: onerror + job_mult_time: 5 + + + somatic_variant_annotation: + path_somatic_variant_calling: ../somatic_variant_calling # REQUIRED + tools: ["vep"] + vep: + cache_dir: {{ params["vep_cache"] }} + assembly: GRCh37 + + + somatic_variant_filtration: + path_somatic_variant: ../somatic_variant_annotation + path_ngs_mapping: ../ngs_mapping + filter_list: + - dkfz: {} + - bcftools: + exclude: FORMAT/DP[1]<=50 | AD[1:1]<5 | AD[1:1]/(AD[1:0]+AD[1:1])<0.025 + + + +data_sets: + trbc: + file: samplesheet.tsv + search_patterns: + - {left: '*.R1.fastq.gz', right: '*.R2.fastq.gz'} + search_paths: + - ../raw + type: matched_cancer + naming_scheme: only_secondary_id diff --git a/.tests/test-workflow/config/config.yaml b/.tests/test-workflow/config/config.yaml new file mode 100644 index 000000000..f45282f7f --- /dev/null +++ b/.tests/test-workflow/config/config.yaml @@ -0,0 +1,12 @@ +reference: + species: "homo_sapiens" + datatype: "dna" + build: "GRCh37" + release: 111 + chromosome: "12" + +pipeline-configuration: + cancer_wes: + workdir: "pipelines/snappy-cancer_wes" + config: "pipelines/snappy-cancer_wes/.snappy_pipeline/config.yaml" + samplesheet: "pipelines/snappy-cancer_wes/.snappy_pipeline/samplesheet.tsv" diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/.gitattributes b/.tests/test-workflow/pipelines/snappy-cancer_wes/.gitattributes new file mode 100644 index 000000000..44de6a0dd --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/.gitattributes @@ -0,0 +1 @@ +raw filter=lfs diff=lfs merge=lfs -text diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/.snappy_pipeline/samplesheet.tsv b/.tests/test-workflow/pipelines/snappy-cancer_wes/.snappy_pipeline/samplesheet.tsv new file mode 100644 index 000000000..0548acece --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/.snappy_pipeline/samplesheet.tsv @@ -0,0 +1,15 @@ +[Metadata] +schema cancer_matched +schema_version v1 +title TRCB +description Public cancer dataset https://www.nature.com/articles/sdata201610 + +[Custom Fields] +key annotatedEntity docs type minimum maximum unit choices pattern +extractionType bioSample extraction type string 0 0 0 0 0 +libraryKit ngsLibrary exome enrichment kit string 0 0 0 0 0 + +[Data] +patientName sampleName isTumor extractionType libraryType folderName libraryKit +case001subregion N1 N DNA WES case001subregion-N1-DNA1-WES1 MedExome +case001subregion T1 Y DNA WES case001subregion-T1-DNA1-WES1 MedExome diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/config.yaml b/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/config.yaml new file mode 100644 index 000000000..4b641f38f --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/config.yaml @@ -0,0 +1,5 @@ +pipeline_step: + name: ngs_mapping + version: 1 + +$ref: 'file://../.snappy_pipeline/config.yaml' diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/pipeline_job.sh b/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/pipeline_job.sh new file mode 100644 index 000000000..2d0ae8d8e --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/ngs_mapping/pipeline_job.sh @@ -0,0 +1,135 @@ +#!/bin/bash + +# SNAPPY best practice pipeline_job.sh +# +# Version: 3 +# Date: 2017-02-02 + +# The medium project/queue is a sensible default. +#SBATCH --partition medium +# Set a required running time for the master job. +#SBATCH --time 3-00 +# Reserve some resources +#SBATCH --mem=6G +# Keep current environment variables +#SBATCH --export=all +# Send a mail upon job completion and error +##SBATCH --mail-type ALL +##SBATCH --mail-user your.name@mdc-berlin.de +# Logs should be written into "slurm_log" sub directory. +#SBATCH --output slurm_log/%x-%J.log +# Use more descriptive name in Slurm. +#SBATCH --job-name ngs_mapping + +# Enable the official bash strict mode (fail early, fail often) +set -euo pipefail + +# Fix the umask. +umask ug=rwx,o= + +# Configuration variables --------------------------------------------------- + +# Maximal number of jobs to execute at the same time +MAX_JOBS=500 +# Maximal number of jobs per second +MAX_JOBS_PER_SECOND=10 +# Number of times to restart jobs +RESTART_TIMES=0 + +# Check preconditions ------------------------------------------------------- + +# Ensure slurm_log is a directory +test -d slurm_log || { >&2 echo "${PWD}/slurm_log does not exist"; exit 1; } + +# Enforce existence of TMPDIR ----------------------------------------------- + +export TMPDIR=${HOME}/scratch/tmp +mkdir -p ${TMPDIR} + +# Create one log directory per Snakemake run -------------------------------- + +test -z "${SLURM_JOB_ID-}" && SLURM_JOB_ID=$(date +%Y-%m-%d_%H-%M) +LOGDIR=slurm_log/${SLURM_JOB_ID} +mkdir -p ${LOGDIR} +export SBATCH_DEFAULTS=" --output=${LOGDIR}/%x-%j.log" + +# Activate appropriate Miniconda3 installation ------------------------------ + +# 1. If CONDA_PATH is set, use this. +# 2. Look into parent directories for miniconda3 (owned by current user) +# 3. Look whether there is a conda in $PATH and use it. +# 4. Look for ~/miniconda3 and use it +# 5. If all fails, bail out. + +conda-in-parent() +{ + current=$PWD + while [[ -n "$current" ]] && [[ "$current" != "/" ]]; do + if [[ -e "$current/miniconda3.$USER" ]] && \ + [[ $(stat -c %u $current/miniconda3.$USER) == $UID ]]; then + echo "$current/miniconda3.$USER" + return 0 + fi + if [[ -e "$current/miniconda3" ]] && \ + [[ $(stat -c %u $current/miniconda3) == $UID ]]; then + echo "$current/miniconda3" + return 0 + fi + current=$(dirname $current) + done + + return 1 +} + +if [[ -n "${CONDA_PATH-}" ]] || CONDA_PATH=$(conda-in-parent); then + : +elif which conda >/dev/null; then + CONDA_PATH=$(dirname $(dirname $(which conda))) +elif [[ -e $HOME/miniconda3 ]]; then + CONDA_PATH=$HOME/miniconda3 +elif [[ -e $HOME/work/miniconda3 ]]; then + CONDA_PATH=$HOME/work/miniconda3 +else + >&2 echo "Could not determine a suitable CONDA_PATH." + exit 1 +fi + +>&2 echo "Using conda installation in $CONDA_PATH" +>&2 echo "+ conda activate " +set +euo pipefail +conda deactivate &>/dev/null || true # disable any existing +source $CONDA_PATH/etc/profile.d/conda.sh +conda activate # enable found +set -euo pipefail + +# Activate bash cmd printing, debug info ------------------------------------ + +set -x +>&2 hostname +>&2 date + +# Kick off Snakemake -------------------------------------------------------- + +# Interpret array jobs. +# Allow selection of batch +if [[ ! -z "${SNAPPY_BATCH-}" ]]; then + SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}" +else + SNAKEMAKE_BATCH_ARG= +fi + +# Using the medium project/queue is a sensible default. +snappy-snake --printshellcmds \ + ${SNAKEMAKE_BATCH_ARG} \ + --snappy-pipeline-use-profile "cubi-v1" \ + --snappy-pipeline-jobs $MAX_JOBS \ + --restart-times ${RESTART_TIMES} \ + --default-partition="medium" \ + --rerun-incomplete \ + -- \ + $* + +# Print date after finishing, for good measure ------------------------------ + +>&2 date +>&2 echo "All done. Have a nice day." diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/raw/case001subregion-N1-DNA1-WES1/case001subregion-N1-DNA1-WES1.R1.fastq.gz b/.tests/test-workflow/pipelines/snappy-cancer_wes/raw/case001subregion-N1-DNA1-WES1/case001subregion-N1-DNA1-WES1.R1.fastq.gz new file mode 100644 index 000000000..c8135cbd8 --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/raw/case001subregion-N1-DNA1-WES1/case001subregion-N1-DNA1-WES1.R1.fastq.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7b2d9c394285f445bb37dc263f5c8531fc44a6c32cefaef218f19dc076039fec +size 7325125 diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/raw/case001subregion-N1-DNA1-WES1/case001subregion-N1-DNA1-WES1.R2.fastq.gz b/.tests/test-workflow/pipelines/snappy-cancer_wes/raw/case001subregion-N1-DNA1-WES1/case001subregion-N1-DNA1-WES1.R2.fastq.gz new file mode 100644 index 000000000..9606dfd8e --- /dev/null +++ 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7188610 C1R +12 7189266 7189457 C1R +12 7241137 7241644 C1R +12 7241800 7242430 C1R +12 7242573 7242910 C1R +12 7243973 7244482 C1R +12 7244935 7245047 C1R +12 7246177 7246605 C1RL +12 7248944 7249786 C1RL +12 7252012 7252724 C1RL +12 7254345 7254761 C1RL +12 7260764 7261130 C1RL +12 7261638 7261890 C1RL +12 7276653 7276831 RBP5 +12 7277152 7277403 RBP5 +12 7280141 7280475 RBP5 +12 7280761 7281044 RBP5 +12 7281216 7281501 RBP5 +12 7283163 7283363 CLSTN3 +12 7284314 7284561 CLSTN3 +12 7285416 7285809 CLSTN3 +12 7286104 7286420 CLSTN3 +12 7287864 7288205 CLSTN3 +12 7288293 7289108 CLSTN3 +12 7289314 7289818 CLSTN3 +12 7290467 7290738 CLSTN3 +12 7293741 7294091 CLSTN3 +12 7294589 7294832 CLSTN3 +12 7295396 7296035 CLSTN3 +12 7301511 7301856 CLSTN3 +12 7302029 7302350 CLSTN3 +12 7303089 7303728 CLSTN3 +12 7308743 7309653 CLSTN3 +12 7310021 7310319 CLSTN3 +12 7310456 7310789 CLSTN3 +12 7342490 7342638 PEX5 +12 7342842 7343301 PEX5 +12 7343347 7343649 PEX5 +12 7343742 7344011 PEX5 +12 7344103 7344387 PEX5 +12 7351504 7351794 PEX5 +12 7354190 7354536 PEX5 +12 7354743 7355011 PEX5 +12 7355100 7355368 PEX5 +12 7355975 7356244 PEX5 +12 7360203 7360817 PEX5 +12 7360964 7361333 PEX5 +12 7361561 7361814 PEX5 +12 7362197 7362893 PEX5 +12 7456857 7457201 ACSM4 +12 7459055 7459399 ACSM4 +12 7463081 7463398 ACSM4 +12 7469670 7469930 ACSM4 +12 7470578 7470827 ACSM4 +12 7473220 7473511 ACSM4 +12 7474914 7475241 ACSM4 +12 7475758 7476211 ACSM4 +12 7476821 7477274 ACSM4 +12 7479465 7479774 ACSM4 +12 7480774 7481074 ACSM4 +12 7509872 7510201 CD163L1 +12 7519803 7519950 CD163L1 +12 7520595 7520930 CD163L1 +12 7521407 7521763 CD163L1 +12 7521908 7522305 CD163L1 +12 7525836 7526274 CD163L1 +12 7526986 7527613 CD163L1 +12 7527793 7528677 CD163L1 +12 7531534 7531961 CD163L1 +12 7548626 7549079 CD163L1 +12 7550811 7551261 CD163L1 +12 7556038 7556514 CD163L1 +12 7559049 7559546 CD163L1 +12 7584937 7585424 CD163L1 +12 7585865 7586344 CD163L1 +12 7591317 7592593 CD163L1 +12 7593675 7593931 CD163L1 +12 7596622 7596798 CD163L1 +12 7632361 7632671 CD163 +12 7633689 7633915 CD163 +12 7635152 7635688 CD163 +12 7635928 7636343 CD163 +12 7637620 7638112 CD163 +12 7639040 7639662 CD163 +12 7639885 7640716 CD163 +12 7647598 7648054 CD163 +12 7649342 7649794 CD163 +12 7651372 7651849 CD163 +12 7653684 7654149 CD163 +12 7654964 7655477 CD163 +12 7656183 7656347 CD163 +12 7759516 7759713 RP11-444J21.2 +12 7802054 7802376 APOBEC1 +12 7803559 7803830 APOBEC1 +12 7804973 7805516 APOBEC1 +12 7807080 7807335 APOBEC1 +12 7818295 7818594 APOBEC1 +12 7842384 7843365 GDF3 +12 7847969 7848398 GDF3 +12 7864055 7864314 DPPA3 +12 7867686 7868094 DPPA3 +12 7868638 7868989 DPPA3 +12 7869533 7869720 DPPA3 +12 7882152 7882409 CLEC4C +12 7883282 7883641 CLEC4C +12 7889989 7890239 CLEC4C +12 7893963 7894189 CLEC4C +12 7898826 7899148 CLEC4C +12 7899770 7900082 CLEC4C +12 7917747 7917923 NANOGNB +12 7922618 7923210 NANOGNB +12 7926403 7926647 NANOGNB +12 7942136 7942497 NANOG +12 7945460 7945917 NANOG 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8387131 FAM86FP +12 8387771 8388423 FAM86FP +12 8389571 8389692 FAM86FP +12 8391154 8391438 FAM86FP +12 8393188 8393362 FAM86FP +12 8439549 8439704 ENPP7P5 +12 8512037 8512325 RPS3AP43 +12 8519248 8519526 RP11-113C12.4 +12 8542854 8543034 LINC00937 +12 8543517 8543759 LINC00937 +12 8549612 8549829 . +12 8608574 8608853 CLEC6A +12 8610404 8610666 CLEC6A +12 8612114 8612360 CLEC6A +12 8618029 8618287 CLEC6A +12 8628667 8628913 CLEC6A +12 8629818 8630187 CLEC6A +12 8666226 8666429 CLEC4D +12 8667765 8667976 CLEC4D +12 8670668 8671015 CLEC4D +12 8671522 8671837 CLEC4D +12 8672727 8673036 CLEC4D +12 8673643 8673953 CLEC4D +12 8687146 8687475 CLEC4E +12 8688634 8688853 CLEC4E +12 8689613 8689996 CLEC4E +12 8691686 8691993 CLEC4E +12 8692340 8692644 CLEC4E +12 8693257 8693484 CLEC4E +12 8756772 8757011 AICDA +12 8757355 8757539 AICDA +12 8757770 8758153 AICDA +12 8759353 8759698 AICDA +12 8765260 8765460 AICDA +12 8787627 8788035 RP11-438L7.3 +12 8789299 8790016 MFAP5 +12 8800590 8800908 MFAP5 +12 8802010 8802254 MFAP5 +12 8803014 8803262 MFAP5 +12 8804158 8804368 MFAP5 +12 8806929 8807214 MFAP5 +12 8807909 8808151 MFAP5 +12 8808279 8808538 MFAP5 +12 8814517 8814823 MFAP5 +12 8850757 8850995 RIMKLB +12 8866342 8866730 RIMKLB +12 8902387 8902789 RIMKLB +12 8904471 8904727 RIMKLB +12 8906429 8906750 RIMKLB +12 8925888 8926463 RIMKLB +12 8929293 8929458 RIMKLB +12 8930122 8930355 RIMKLB +12 8955320 8955441 A2ML1-AS1 +12 8975186 8975384 A2ML1 +12 8975702 8976069 A2ML1 +12 8976265 8976558 A2ML1 +12 8982266 8982494 A2ML1 +12 8987170 8987353 A2ML1 +12 8988017 8988355 A2ML1 +12 8988795 8988990 A2ML1 +12 8989971 8990237 A2ML1 +12 8990851 8991153 A2ML1 +12 8991659 8991890 A2ML1 +12 8993894 8994195 A2ML1 +12 8995655 8996054 A2ML1 +12 8997673 8998162 A2ML1 +12 8998612 8998907 A2ML1 +12 9000032 9000381 A2ML1 +12 9001230 9001579 A2ML1 +12 9002171 9002458 A2ML1 +12 9002614 9002970 A2ML1 +12 9004330 9005017 A2ML1 +12 9006662 9006920 A2ML1 +12 9007270 9007507 A2ML1 +12 9008016 9008285 A2ML1 +12 9009707 9010279 A2ML1 +12 9010498 9010778 A2ML1 +12 9013450 9013613 A2ML1 +12 9013641 9013957 A2ML1 +12 9016320 9016694 A2ML1 +12 9020364 9021323 A2ML1 +12 9021631 9021871 A2ML1 +12 9026924 9027191 A2ML1 +12 9027453 9027739 A2ML1 +12 9070168 9070501 PHC1 +12 9072222 9072572 PHC1 +12 9073486 9073768 PHC1 +12 9074113 9074448 PHC1 +12 9075140 9075455 PHC1 +12 9082949 9083330 PHC1 +12 9083341 9083619 PHC1 +12 9085071 9086074 PHC1 +12 9086364 9087161 PHC1 +12 9087638 9087937 PHC1 +12 9089354 9090018 PHC1 +12 9090350 9090736 PHC1 +12 9091797 9092147 PHC1 +12 9092313 9092620 PHC1 +12 9093248 9093566 PHC1 +12 9093248 9093566 M6PR +12 9094321 9094588 M6PR +12 9094915 9095229 M6PR +12 9095891 9096222 M6PR +12 9096346 9096581 M6PR +12 9097893 9098261 M6PR +12 9098754 9099075 M6PR +12 9142104 9142462 KLRG1 +12 9144740 9144945 KLRG1 +12 9147615 9147980 KLRG1 +12 9161514 9161721 KLRG1 +12 9161944 9162236 KLRG1 +12 9162464 9162740 KLRG1 +12 9180557 9180678 HNRNPA1P34 +12 9210644 9210802 LINC00612 +12 9220340 9220872 A2M +12 9221271 9221467 A2M +12 9222261 9222492 A2M +12 9222970 9223268 A2M +12 9224874 9225546 A2M +12 9227088 9227469 A2M +12 9229258 9229667 A2M +12 9229851 9230138 A2M +12 9230183 9230536 A2M +12 9231746 9232014 A2M +12 9232150 9232505 A2M +12 9232601 9232840 A2M +12 9241698 9241948 A2M +12 9242400 9242690 A2M +12 9242848 9243134 A2M +12 9243709 9244101 A2M +12 9245983 9246176 A2M +12 9247517 9247763 A2M +12 9248038 9248360 A2M +12 9251117 9251438 A2M +12 9251893 9252200 A2M +12 9253636 9253916 A2M +12 9253963 9254358 A2M +12 9256758 9257079 A2M +12 9258756 9259248 A2M +12 9260039 9260307 A2M +12 9261802 9262107 A2M +12 9262400 9262679 A2M +12 9262805 9263015 A2M +12 9264662 9265208 A2M +12 9265856 9266222 A2M +12 9268273 9268558 A2M +12 9301455 9301678 PZP +12 9302038 9302324 PZP +12 9303166 9303405 PZP +12 9304095 9304356 PZP +12 9304732 9304975 PZP +12 9305356 9306026 PZP +12 9307120 9307527 PZP +12 9309709 9310016 PZP +12 9310267 9310531 PZP +12 9310897 9311264 PZP +12 9312443 9312710 PZP +12 9312846 9313158 PZP +12 9313550 9313802 PZP +12 9315053 9315360 PZP +12 9316161 9316453 PZP +12 9316606 9316937 PZP +12 9317633 9318045 PZP +12 9318577 9318857 PZP +12 9321406 9321645 PZP +12 9321935 9322255 PZP +12 9333480 9333863 PZP +12 9334500 9334769 PZP +12 9344676 9344959 PZP +12 9345037 9345397 PZP +12 9346590 9346902 PZP +12 9348858 9349373 PZP +12 9349488 9349827 PZP +12 9352892 9353129 PZP +12 9353401 9353728 PZP +12 9353813 9354034 PZP +12 9354846 9355327 PZP +12 9356293 9356624 PZP +12 9360755 9361048 PZP +12 9391945 9392213 A2MP1 +12 9392605 9392985 PTMAP4 +12 9440438 9441043 RP11-22B23.1 +12 9446198 9446589 RP11-22B23.1 +12 9446997 9447215 RP11-22B23.1 +12 9447280 9447732 RP11-22B23.1 +12 9450978 9451167 RP11-22B23.1 +12 9451342 9451501 RP11-22B23.1 +12 9451749 9452190 RP11-22B23.1 +12 9453584 9453969 RP11-22B23.1 +12 9454712 9454918 RP11-22B23.1 +12 9455177 9455336 RP11-22B23.1 +12 9456407 9456769 RP11-22B23.1 +12 9458158 9459098 RP11-22B23.1 +12 9459665 9460068 RP11-22B23.1 +12 9462434 9462750 RP11-22B23.1 +12 9462866 9463115 RP11-22B23.1 +12 9464005 9464462 RP11-22B23.1 +12 9464718 9465064 RP11-22B23.1 +12 9465102 9466111 RP11-22B23.1 +12 9550224 9550316 . +12 9550994 9551049 RP11-599J14.2 +12 9552323 9553026 RP11-599J14.2 +12 9554260 9554559 RP11-599J14.2 +12 9554903 9555259 RP11-599J14.2 +12 9557294 9557411 RP11-599J14.2 +12 9570889 9571563 DDX12P +12 9571948 9572275 DDX12P +12 9572537 9572939 DDX12P +12 9573083 9573270 DDX12P +12 9573870 9574159 DDX12P +12 9574271 9574589 DDX12P +12 9576981 9577345 DDX12P +12 9577886 9578864 DDX12P +12 9580153 9580620 DDX12P +12 9581694 9581857 DDX12P +12 9582032 9582323 DDX12P +12 9583075 9583393 DDX12P +12 9584809 9585324 DDX12P +12 9585480 9585640 DDX12P +12 9585865 9586048 DDX12P +12 9586523 9586892 DDX12P +12 9589415 9589818 DDX12P +12 9589873 9590182 DDX12P +12 9590530 9590915 DDX12P +12 9596131 9596638 DDX12P +12 9659290 9659345 RP11-525E9.1 +12 9659593 9659936 RP11-525E9.1 +12 9659997 9660399 RP11-525E9.1 +12 9664218 9664515 RP11-726G1.1 +12 9665303 9665657 RP11-726G1.1 +12 9666053 9666251 RP11-726G1.1 +12 9669507 9669810 RP11-726G1.1 +12 9670177 9670541 RP11-726G1.1 +12 9670709 9670960 RP11-726G1.1 +12 9671554 9671846 RP11-726G1.1 +12 9672664 9672892 RP11-726G1.1 +12 9684145 9684400 RP11-726G1.1 +12 9685112 9685300 RP11-726G1.1 +12 9688741 9688966 RP11-726G1.1 +12 9692916 9693159 RP11-726G1.1 +12 9693761 9693965 RP11-726G1.1 +12 9694222 9694498 RP11-726G1.1 +12 9695085 9695426 RP11-726G1.1 +12 9697569 9697768 RP11-726G1.1 +12 9698130 9698417 RP11-726G1.1 +12 9703990 9704261 RP11-726G1.1 +12 9704959 9705260 RP11-726G1.1 +12 9706515 9706757 RP11-726G1.1 +12 9707052 9707399 RP11-726G1.1 +12 9707542 9707803 RP11-726G1.1 +12 9709233 9709477 RP11-726G1.1 +12 9710038 9710258 RP11-726G1.1 +12 9710883 9711146 RP11-726G1.1 +12 9711743 9711955 RP11-726G1.1 +12 9712627 9712831 RP11-726G1.1 +12 9713442 9713606 RP11-726G1.1 +12 9716763 9716939 RP11-726G1.1 +12 9717652 9717918 RP11-726G1.1 +12 9723314 9723571 RP11-726G1.1 +12 9723987 9724247 RP11-726G1.1 +12 9725543 9725780 RP11-726G1.1 +12 9725841 9726177 RP11-726G1.1 +12 9747820 9748073 KLRB1 +12 9750555 9750838 KLRB1 +12 9751061 9751274 KLRB1 +12 9752323 9752479 KLRB1 +12 9753998 9754247 KLRB1 +12 9760252 9760528 KLRB1 +12 9794767 9794856 RP11-705C15.2 +12 9822245 9822481 CLEC2D +12 9833474 9833703 CLEC2D +12 9840433 9840729 CLEC2D +12 9845341 9845819 CLEC2D +12 9846300 9846432 CLEC2D +12 9847266 9847589 CLEC2D +12 9848208 9848301 RP11-75L1.2 +12 9848442 9848592 RP11-75L1.2 +12 9848780 9848987 RP11-75L1.2 +12 9849254 9849486 . +12 9861473 9861603 RP11-75L1.1 +12 9869248 9869462 CLECL1 +12 9871231 9871442 CLECL1 +12 9875174 9875461 CLECL1 +12 9885491 9885951 CLECL1 +12 9906047 9906237 CD69 +12 9907101 9907348 CD69 +12 9907623 9907911 CD69 +12 9908789 9909125 CD69 +12 9913320 9913432 CD69 +12 9969969 9970448 RP11-75L1.6 +12 9980062 9980312 KLRF1 +12 9984855 9985052 KLRF1 +12 9985843 9986135 KLRF1 +12 9994356 9994599 KLRF1 +12 9994846 9995114 KLRF1 +12 9996966 9997207 KLRF1 +12 10005829 10006089 CLEC2B +12 10006874 10007173 CLEC2B +12 10010004 10010298 CLEC2B +12 10015032 10015232 CLEC2B +12 10034156 10034298 KLRF2 +12 10037487 10037672 KLRF2 +12 10041255 10041481 KLRF2 +12 10045528 10045880 KLRF2 +12 10045929 10046236 KLRF2 +12 10048206 10048539 KLRF2 +12 10051436 10051614 CLEC2A +12 10066086 10066381 CLEC2A +12 10069214 10069467 CLEC2A +12 10074644 10074853 CLEC2A +12 10078793 10079023 CLEC2A +12 10084823 10085007 CLEC2A +12 10103841 10104048 CLEC12A +12 10124090 10124421 CLEC12A +12 10131528 10131679 CLEC12A +12 10131859 10132200 CLEC12A +12 10133099 10133444 CLEC12A +12 10134586 10134804 CLEC12A +12 10136060 10136198 CLEC12A +12 10137400 10137640 CLEC12A +12 10138684 10138783 CLEC1B +12 10145664 10145891 CLEC1B +12 10147576 10147943 CLEC1B +12 10149394 10149922 CLEC1B +12 10150786 10151050 CLEC1B +12 10151586 10151744 CLEC1B +12 10163317 10163515 CLEC12B +12 10165298 10165563 CLEC12B +12 10167073 10167414 CLEC12B +12 10167791 10168097 CLEC12B +12 10168127 10168417 CLEC12B +12 10170897 10171138 CLEC12B +12 10191672 10191886 CLEC9A +12 10205235 10205422 CLEC9A +12 10206802 10207012 CLEC9A +12 10213667 10213975 CLEC9A +12 10215591 10215875 CLEC9A +12 10217243 10217547 CLEC9A +12 10218053 10218277 CLEC9A +12 10223900 10224191 CLEC1A +12 10225833 10226090 CLEC1A +12 10228046 10228324 CLEC1A +12 10233799 10234104 CLEC1A +12 10241629 10241901 CLEC1A +12 10251326 10251617 CLEC1A +12 10264295 10265096 HNRNPABP1 +12 10271000 10271273 CLEC7A +12 10275779 10276025 CLEC7A +12 10277723 10278105 CLEC7A +12 10279097 10279360 CLEC7A +12 10279502 10280482 CLEC7A +12 10282493 10282756 CLEC7A +12 10312400 10312712 OLR1 +12 10312857 10313174 OLR1 +12 10313334 10313559 OLR1 +12 10319238 10319608 OLR1 +12 10321617 10321821 OLR1 +12 10324538 10324730 OLR1 +12 10332157 10332236 TMEM52B +12 10335066 10335276 TMEM52B +12 10337894 10338018 TMEM52B +12 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58025954 B4GALNT1 +12 58087899 58088131 OS9 +12 58088484 58088782 OS9 +12 58089534 58089894 OS9 +12 58109495 58110014 OS9 +12 58110194 58110264 OS9 +12 58110475 58110559 OS9 +12 58111636 58111807 OS9 +12 58111888 58112235 OS9 +12 58112734 58113032 OS9 +12 58113818 58114090 OS9 +12 58114129 58114374 OS9 +12 58114597 58114718 OS9 +12 58120836 58120890 AGAP2 +12 58121194 58121387 AGAP2 +12 58121739 58121843 AGAP2 +12 58122010 58122228 AGAP2 +12 58123425 58123480 AGAP2 +12 58124238 58124407 AGAP2 +12 58124566 58124760 AGAP2 +12 58125076 58125494 AGAP2 +12 58125586 58125804 AGAP2 +12 58126590 58126724 AGAP2 +12 58127797 58127965 AGAP2 +12 58128042 58128228 AGAP2 +12 58131000 58131327 AGAP2 +12 58135629 58135863 AGAP2 +12 58139524 58139670 TSPAN31 +12 58139879 58140112 TSPAN31 +12 58140305 58140564 TSPAN31 +12 58140767 58141103 TSPAN31 +12 58142259 58142564 CDK4 +12 58142848 58143323 CDK4 +12 58144358 58145202 CDK4 +12 58145203 58145547 CDK4 +12 58151691 58152128 MARCH9 +12 58152289 58152691 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b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_annotation/config.yaml new file mode 100644 index 000000000..b79196050 --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_annotation/config.yaml @@ -0,0 +1,5 @@ +pipeline_step: + name: somatic_variant_annotation + version: 1 + +$ref: 'file://../.snappy_pipeline/config.yaml' diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_annotation/pipeline_job.sh b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_annotation/pipeline_job.sh new file mode 100644 index 000000000..e60668737 --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_annotation/pipeline_job.sh @@ -0,0 +1,135 @@ +#!/bin/bash + +# SNAPPY best practice pipeline_job.sh +# +# Version: 3 +# Date: 2017-02-02 + +# The medium project/queue is a sensible default. +#SBATCH --partition medium +# Set a required running time for the master job. +#SBATCH --time 3-00 +# Reserve some resources +#SBATCH --mem=6G +# Keep current environment variables +#SBATCH --export=all +# Send a mail upon job completion and error +##SBATCH --mail-type ALL +##SBATCH --mail-user your.name@mdc-berlin.de +# Logs should be written into "slurm_log" sub directory. +#SBATCH --output slurm_log/%x-%J.log +# Use more descriptive name in Slurm. +#SBATCH --job-name somatic_variant_annotation + +# Enable the official bash strict mode (fail early, fail often) +set -euo pipefail + +# Fix the umask. +umask ug=rwx,o= + +# Configuration variables --------------------------------------------------- + +# Maximal number of jobs to execute at the same time +MAX_JOBS=500 +# Maximal number of jobs per second +MAX_JOBS_PER_SECOND=10 +# Number of times to restart jobs +RESTART_TIMES=0 + +# Check preconditions ------------------------------------------------------- + +# Ensure slurm_log is a directory +test -d slurm_log || { >&2 echo "${PWD}/slurm_log does not exist"; exit 1; } + +# Enforce existence of TMPDIR ----------------------------------------------- + +export TMPDIR=${HOME}/scratch/tmp +mkdir -p ${TMPDIR} + +# Create one log directory per Snakemake run -------------------------------- + +test -z "${SLURM_JOB_ID-}" && SLURM_JOB_ID=$(date +%Y-%m-%d_%H-%M) +LOGDIR=slurm_log/${SLURM_JOB_ID} +mkdir -p ${LOGDIR} +export SBATCH_DEFAULTS=" --output=${LOGDIR}/%x-%j.log" + +# Activate appropriate Miniconda3 installation ------------------------------ + +# 1. If CONDA_PATH is set, use this. +# 2. Look into parent directories for miniconda3 (owned by current user) +# 3. Look whether there is a conda in $PATH and use it. +# 4. Look for ~/miniconda3 and use it +# 5. If all fails, bail out. + +conda-in-parent() +{ + current=$PWD + while [[ -n "$current" ]] && [[ "$current" != "/" ]]; do + if [[ -e "$current/miniconda3.$USER" ]] && \ + [[ $(stat -c %u $current/miniconda3.$USER) == $UID ]]; then + echo "$current/miniconda3.$USER" + return 0 + fi + if [[ -e "$current/miniconda3" ]] && \ + [[ $(stat -c %u $current/miniconda3) == $UID ]]; then + echo "$current/miniconda3" + return 0 + fi + current=$(dirname $current) + done + + return 1 +} + +if [[ -n "${CONDA_PATH-}" ]] || CONDA_PATH=$(conda-in-parent); then + : +elif which conda >/dev/null; then + CONDA_PATH=$(dirname $(dirname $(which conda))) +elif [[ -e $HOME/miniconda3 ]]; then + CONDA_PATH=$HOME/miniconda3 +elif [[ -e $HOME/work/miniconda3 ]]; then + CONDA_PATH=$HOME/work/miniconda3 +else + >&2 echo "Could not determine a suitable CONDA_PATH." + exit 1 +fi + +>&2 echo "Using conda installation in $CONDA_PATH" +>&2 echo "+ conda activate " +set +euo pipefail +conda deactivate &>/dev/null || true # disable any existing +source $CONDA_PATH/etc/profile.d/conda.sh +conda activate # enable found +set -euo pipefail + +# Activate bash cmd printing, debug info ------------------------------------ + +set -x +>&2 hostname +>&2 date + +# Kick off Snakemake -------------------------------------------------------- + +# Interpret array jobs. +# Allow selection of batch +if [[ ! -z "${SNAPPY_BATCH-}" ]]; then + SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}" +else + SNAKEMAKE_BATCH_ARG= +fi + +# Using the medium project/queue is a sensible default. +snappy-snake --printshellcmds \ + ${SNAKEMAKE_BATCH_ARG} \ + --snappy-pipeline-use-profile "cubi-v1" \ + --snappy-pipeline-jobs $MAX_JOBS \ + --restart-times ${RESTART_TIMES} \ + --default-partition="medium" \ + --rerun-incomplete \ + -- \ + $* + +# Print date after finishing, for good measure ------------------------------ + +>&2 date +>&2 echo "All done. Have a nice day." diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/config.yaml b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/config.yaml new file mode 100644 index 000000000..ca34e30fe --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/config.yaml @@ -0,0 +1,5 @@ +pipeline_step: + name: somatic_variant_calling + version: 1 + +$ref: 'file://../.snappy_pipeline/config.yaml' diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/pipeline_job.sh b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/pipeline_job.sh new file mode 100644 index 000000000..a660c791e --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_calling/pipeline_job.sh @@ -0,0 +1,135 @@ +#!/bin/bash + +# SNAPPY best practice pipeline_job.sh +# +# Version: 3 +# Date: 2017-02-02 + +# The medium project/queue is a sensible default. +#SBATCH --partition medium +# Set a required running time for the master job. +#SBATCH --time 3-00 +# Reserve some resources +#SBATCH --mem=6G +# Keep current environment variables +#SBATCH --export=all +# Send a mail upon job completion and error +##SBATCH --mail-type ALL +##SBATCH --mail-user your.name@mdc-berlin.de +# Logs should be written into "slurm_log" sub directory. +#SBATCH --output slurm_log/%x-%J.log +# Use more descriptive name in Slurm. +#SBATCH --job-name somatic_variant_calling + +# Enable the official bash strict mode (fail early, fail often) +set -euo pipefail + +# Fix the umask. +umask ug=rwx,o= + +# Configuration variables --------------------------------------------------- + +# Maximal number of jobs to execute at the same time +MAX_JOBS=500 +# Maximal number of jobs per second +MAX_JOBS_PER_SECOND=10 +# Number of times to restart jobs +RESTART_TIMES=0 + +# Check preconditions ------------------------------------------------------- + +# Ensure slurm_log is a directory +test -d slurm_log || { >&2 echo "${PWD}/slurm_log does not exist"; exit 1; } + +# Enforce existence of TMPDIR ----------------------------------------------- + +export TMPDIR=${HOME}/scratch/tmp +mkdir -p ${TMPDIR} + +# Create one log directory per Snakemake run -------------------------------- + +test -z "${SLURM_JOB_ID-}" && SLURM_JOB_ID=$(date +%Y-%m-%d_%H-%M) +LOGDIR=slurm_log/${SLURM_JOB_ID} +mkdir -p ${LOGDIR} +export SBATCH_DEFAULTS=" --output=${LOGDIR}/%x-%j.log" + +# Activate appropriate Miniconda3 installation ------------------------------ + +# 1. If CONDA_PATH is set, use this. +# 2. Look into parent directories for miniconda3 (owned by current user) +# 3. Look whether there is a conda in $PATH and use it. +# 4. Look for ~/miniconda3 and use it +# 5. If all fails, bail out. + +conda-in-parent() +{ + current=$PWD + while [[ -n "$current" ]] && [[ "$current" != "/" ]]; do + if [[ -e "$current/miniconda3.$USER" ]] && \ + [[ $(stat -c %u $current/miniconda3.$USER) == $UID ]]; then + echo "$current/miniconda3.$USER" + return 0 + fi + if [[ -e "$current/miniconda3" ]] && \ + [[ $(stat -c %u $current/miniconda3) == $UID ]]; then + echo "$current/miniconda3" + return 0 + fi + current=$(dirname $current) + done + + return 1 +} + +if [[ -n "${CONDA_PATH-}" ]] || CONDA_PATH=$(conda-in-parent); then + : +elif which conda >/dev/null; then + CONDA_PATH=$(dirname $(dirname $(which conda))) +elif [[ -e $HOME/miniconda3 ]]; then + CONDA_PATH=$HOME/miniconda3 +elif [[ -e $HOME/work/miniconda3 ]]; then + CONDA_PATH=$HOME/work/miniconda3 +else + >&2 echo "Could not determine a suitable CONDA_PATH." + exit 1 +fi + +>&2 echo "Using conda installation in $CONDA_PATH" +>&2 echo "+ conda activate " +set +euo pipefail +conda deactivate &>/dev/null || true # disable any existing +source $CONDA_PATH/etc/profile.d/conda.sh +conda activate # enable found +set -euo pipefail + +# Activate bash cmd printing, debug info ------------------------------------ + +set -x +>&2 hostname +>&2 date + +# Kick off Snakemake -------------------------------------------------------- + +# Interpret array jobs. +# Allow selection of batch +if [[ ! -z "${SNAPPY_BATCH-}" ]]; then + SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}" +else + SNAKEMAKE_BATCH_ARG= +fi + +# Using the medium project/queue is a sensible default. +snappy-snake --printshellcmds \ + ${SNAKEMAKE_BATCH_ARG} \ + --snappy-pipeline-use-profile "cubi-v1" \ + --snappy-pipeline-jobs $MAX_JOBS \ + --restart-times ${RESTART_TIMES} \ + --default-partition="medium" \ + --rerun-incomplete \ + -- \ + $* + +# Print date after finishing, for good measure ------------------------------ + +>&2 date +>&2 echo "All done. Have a nice day." diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/config.yaml b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/config.yaml new file mode 100644 index 000000000..2d85e1ef1 --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/config.yaml @@ -0,0 +1,5 @@ +pipeline_step: + name: somatic_variant_filtration + version: 1 + +$ref: 'file://../.snappy_pipeline/config.yaml' diff --git a/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/pipeline_job.sh b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/pipeline_job.sh new file mode 100644 index 000000000..b6f3b6c45 --- /dev/null +++ b/.tests/test-workflow/pipelines/snappy-cancer_wes/somatic_variant_filtration/pipeline_job.sh @@ -0,0 +1,135 @@ +#!/bin/bash + +# SNAPPY best practice pipeline_job.sh +# +# Version: 3 +# Date: 2017-02-02 + +# The medium project/queue is a sensible default. +#SBATCH --partition medium +# Set a required running time for the master job. +#SBATCH --time 3-00 +# Reserve some resources +#SBATCH --mem=6G +# Keep current environment variables +#SBATCH --export=all +# Send a mail upon job completion and error +##SBATCH --mail-type ALL +##SBATCH --mail-user your.name@mdc-berlin.de +# Logs should be written into "slurm_log" sub directory. +#SBATCH --output slurm_log/%x-%J.log +# Use more descriptive name in Slurm. +#SBATCH --job-name somatic_variant_filtration + +# Enable the official bash strict mode (fail early, fail often) +set -euo pipefail + +# Fix the umask. +umask ug=rwx,o= + +# Configuration variables --------------------------------------------------- + +# Maximal number of jobs to execute at the same time +MAX_JOBS=500 +# Maximal number of jobs per second +MAX_JOBS_PER_SECOND=10 +# Number of times to restart jobs +RESTART_TIMES=0 + +# Check preconditions ------------------------------------------------------- + +# Ensure slurm_log is a directory +test -d slurm_log || { >&2 echo "${PWD}/slurm_log does not exist"; exit 1; } + +# Enforce existence of TMPDIR ----------------------------------------------- + +export TMPDIR=${HOME}/scratch/tmp +mkdir -p ${TMPDIR} + +# Create one log directory per Snakemake run -------------------------------- + +test -z "${SLURM_JOB_ID-}" && SLURM_JOB_ID=$(date +%Y-%m-%d_%H-%M) +LOGDIR=slurm_log/${SLURM_JOB_ID} +mkdir -p ${LOGDIR} +export SBATCH_DEFAULTS=" --output=${LOGDIR}/%x-%j.log" + +# Activate appropriate Miniconda3 installation ------------------------------ + +# 1. If CONDA_PATH is set, use this. +# 2. Look into parent directories for miniconda3 (owned by current user) +# 3. Look whether there is a conda in $PATH and use it. +# 4. Look for ~/miniconda3 and use it +# 5. If all fails, bail out. + +conda-in-parent() +{ + current=$PWD + while [[ -n "$current" ]] && [[ "$current" != "/" ]]; do + if [[ -e "$current/miniconda3.$USER" ]] && \ + [[ $(stat -c %u $current/miniconda3.$USER) == $UID ]]; then + echo "$current/miniconda3.$USER" + return 0 + fi + if [[ -e "$current/miniconda3" ]] && \ + [[ $(stat -c %u $current/miniconda3) == $UID ]]; then + echo "$current/miniconda3" + return 0 + fi + current=$(dirname $current) + done + + return 1 +} + +if [[ -n "${CONDA_PATH-}" ]] || CONDA_PATH=$(conda-in-parent); then + : +elif which conda >/dev/null; then + CONDA_PATH=$(dirname $(dirname $(which conda))) +elif [[ -e $HOME/miniconda3 ]]; then + CONDA_PATH=$HOME/miniconda3 +elif [[ -e $HOME/work/miniconda3 ]]; then + CONDA_PATH=$HOME/work/miniconda3 +else + >&2 echo "Could not determine a suitable CONDA_PATH." + exit 1 +fi + +>&2 echo "Using conda installation in $CONDA_PATH" +>&2 echo "+ conda activate " +set +euo pipefail +conda deactivate &>/dev/null || true # disable any existing +source $CONDA_PATH/etc/profile.d/conda.sh +conda activate # enable found +set -euo pipefail + +# Activate bash cmd printing, debug info ------------------------------------ + +set -x +>&2 hostname +>&2 date + +# Kick off Snakemake -------------------------------------------------------- + +# Interpret array jobs. +# Allow selection of batch +if [[ ! -z "${SNAPPY_BATCH-}" ]]; then + SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}" +else + SNAKEMAKE_BATCH_ARG= +fi + +# Using the medium project/queue is a sensible default. +snappy-snake --printshellcmds \ + ${SNAKEMAKE_BATCH_ARG} \ + --snappy-pipeline-use-profile "cubi-v1" \ + --snappy-pipeline-jobs $MAX_JOBS \ + --restart-times ${RESTART_TIMES} \ + --default-partition="medium" \ + --rerun-incomplete \ + -- \ + $* + +# Print date after finishing, for good measure ------------------------------ + +>&2 date +>&2 echo "All done. Have a nice day." diff --git a/.tests/test-workflow/resources/cache/.gitattributes b/.tests/test-workflow/resources/cache/.gitattributes new file mode 100644 index 000000000..9c009f569 --- /dev/null +++ b/.tests/test-workflow/resources/cache/.gitattributes @@ -0,0 +1 @@ +vep filter=lfs diff=lfs merge=lfs -text diff --git a/.tests/test-workflow/resources/cache/vep/LICENSE b/.tests/test-workflow/resources/cache/vep/LICENSE new file mode 100644 index 000000000..133ef2803 --- /dev/null +++ b/.tests/test-workflow/resources/cache/vep/LICENSE @@ -0,0 +1,202 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute + Copyright [2016-2023] EMBL-European Bioinformatics Institute + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/.tests/test-workflow/resources/cache/vep/README.md b/.tests/test-workflow/resources/cache/vep/README.md new file mode 100644 index 000000000..86bd5d4a8 --- /dev/null +++ b/.tests/test-workflow/resources/cache/vep/README.md @@ -0,0 +1,2 @@ +# Modifications to VEP cache +The files in the `vep/` cache directory are restricted to the region containing KRAS on chr12, i.e. from 25000001-26000000. diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000.gz b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000.gz new file mode 100644 index 000000000..83a5c2deb Binary files /dev/null and b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000.gz differ diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000_reg.gz b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000_reg.gz new file mode 100644 index 000000000..c3e72deb4 Binary files /dev/null and b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/25000001-26000000_reg.gz differ diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz new file mode 100644 index 000000000..c02877f54 Binary files /dev/null and b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz differ diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz.csi b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz.csi new file mode 100644 index 000000000..0d9d7bd78 Binary files /dev/null and b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/12/all_vars.gz.csi differ diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/chr_synonyms.txt b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/chr_synonyms.txt new file mode 100644 index 000000000..ec3eb2942 --- /dev/null +++ b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/chr_synonyms.txt @@ -0,0 +1,845 @@ +HSCHR1_2_CTG31 NW_003315906.1 +HG1211_PATCH NW_003871068.1 +JH720453.1 NW_003871100.1 +HG50_PATCH NW_004504301.1 +GL000203.1 NT_113941.1 +HSCHR19LRC_COX1_CTG1 NW_003571054.1 +CM000668.1 NC_000006.11 +GL000202.1 NT_113921.2 +HG325_PATCH NW_003871059.1 +JH159145.1 NW_003871090.1 +GL383583.1 NW_003315972.1 +HG1442_PATCH NW_004070886.1 +GL383560.1 HG75_PATCH +KE332505.1 NW_004775434.1 +JH159150.3 NW_003871103.3 +HG186_PATCH NW_003315910.1 +GL000235.1 NT_167229.1 +GL383526.1 NW_003315913.1 +GL000248.1 NT_167242.1 +HG995_PATCH NW_003315933.1 +JH720443.2 NW_003871072.2 +GL383582.2 HSCHR22_1_CTG1 +NC_000009.11 chr9 +HG1486_PATCH NW_004070873.1 +CM000679.1 chr17 +GL949742.1 HSCHR5_3_CTG1 +GL949751.1 NW_003571059.1 +HG444_PATCH KE332499.1 +HSCHR9_3_CTG35 NW_003315931.1 +GL877870.2 NW_003571031.1 +NC_000008.10 chr8 +JH720446.1 NW_003871085.1 +HSCHR17_3_CTG4 NW_003315955.1 +GL383543.1 HG544_PATCH +GL383579.1 NW_003315968.1 +HG729_PATCH JH159149.1 +GL000236.1 NT_167230.1 +GL383538.1 NW_003315927.1 +HG1426_PATCH JH720454.3 +CM000670.1 chr8 +CM000677.1 chr15 +CM000686.1 NC_000024.9 +GL000229.1 NT_167223.1 +CM000666.1 NC_000004.11 +HG325_PATCH JH159132.1 +GL383570.1 NW_003315959.1 +JH591185.1 NW_003871082.1 +CM000683.1 NC_000021.8 +HSCHR2_1_CTG1 NW_003315908.1 +GL000216.1 NT_167211.1 +HSCHR5_1_CTG5 NW_003315919.1 +HSCHR17_1_CTG4 NW_003315953.1 +CM000673.1 NC_000011.9 +GL383578.1 HSCHR21_1_CTG1_1 +HG344_PATCH JH720444.2 +HG1699_PATCH NW_004775431.1 +NC_000019.9 chr19 +GL582974.1 HG858_PATCH +HSCHR9_1_CTG35 NW_003315929.1 +NC_000013.10 chr13 +HG1257_PATCH NW_003871064.1 +NC_000012.11 chr12 +JH636053.3 NW_003871056.3 +HG1293_PATCH NW_003871057.1 +HG306_PATCH JH159140.1 +HSCHR21_2_CTG1_1 NW_003315968.1 +HG256_PATCH JH591184.1 +KB021646.2 NW_004166864.2 +JH720454.3 NW_003871101.3 +GL383525.1 HG991_PATCH +GL582977.2 HG730_PATCH +JH591186.1 NW_003871089.1 +GL383534.2 NW_003315922.2 +GL877873.1 HG905_PATCH +GL383574.1 NW_003315963.1 +GL383562.1 NW_003315951.1 +JH806591.1 NW_004070881.1 +GL949753.1 HSCHR19LRC_PGF2_CTG1 +KB663605.1 NW_004504301.1 +KE332499.1 NW_004775430.1 +GL383574.1 HSCHR19_1_CTG3_1 +HSCHR19_2_CTG3 NW_003315964.2 +GL000218.1 NT_113889.1 +HG1479_PATCH NW_004070870.1 +HG1350_HG959_PATCH NW_004775434.1 +GL383580.1 NW_003315969.1 +CM000681.1 NC_000019.9 +GL383568.1 HSCHR18_1_CTG2 +HG414_PATCH NW_003871081.1 +HG1032_PATCH NW_003571034.1 +HSCHR12_1_CTG1 NW_003571049.1 +JH806598.1 NW_004070888.1 +HG1453_PATCH JH806598.1 +GL000201.1 NT_113911.1 +HSCHR22_1_CTG1 NW_003315971.2 +JH720449.1 NW_003871096.1 +15 chr15 +KB663606.1 NW_004504302.1 +JH720448.1 NW_003871095.1 +HSCHR6_MHC_SSTO_CTG1 NT_167249.1 +19 chr19 +JH806582.2 NW_004070872.2 +GL000196.1 NT_113909.1 +CM000675.1 chr13 +GL339450.1 NW_003315925.1 +CM000671.1 chr9 +NC_000022.10 chr22 +HG151_NOVEL_TEST NW_003871074.1 +HSCHR15_1_CTG8 NW_003315944.1 +GL383542.1 NW_003315931.1 +GL383518.1 HSCHR1_1_CTG31 +HSCHR22_1_CTG2 NW_003315972.1 +JH720452.1 NW_003871099.1 +GL383540.1 HSCHR9_1_CTG35 +HG497_PATCH NW_004070876.1 +HSCHR21_3_CTG1_1 NW_003315969.1 +HG299_PATCH NW_003871076.1 +GL383519.1 NW_003315906.1 +JH806584.1 NW_004070874.1 +HSCHR1_3_CTG31 NW_003315907.1 +10 NC_000010.10 +GL877872.1 NW_003571034.1 +HG944_PATCH KB663608.1 +HSCHR4_1_CTG6 NW_003315915.1 +NC_000024.9 chrY +GL949744.1 HG536_PATCH +20 CM000682.1 +HG1091_PATCH NW_003871058.1 +MT NC_012920.1 +HG1591_PATCH KE332502.1 +HG27_PATCH NW_004070866.1 +GL383569.1 NW_003315958.1 +HG979_PATCH KE332501.1 +KB021647.1 NW_004166865.1 +JH806603.1 NW_004070893.1 +GL949745.1 NW_003571047.1 +HSCHR19_1_CTG3_1 NW_003315963.1 +GL000206.1 NT_113945.1 +GL949742.1 NW_003571036.1 +GL000250.1 HSCHR6_MHC_APD_CTG1 +17 NC_000017.10 +JH806597.1 NW_004070887.1 +GL000192.1 NT_167207.1 +HG1208_PATCH JH720446.1 +HG873_PATCH NW_003871082.1 +GL582970.1 HG736_PATCH +JH159137.1 NW_003871074.1 +GL949749.1 HSCHR19LRC_LRC_J_CTG1 +GL949752.1 HSCHR19LRC_PGF1_CTG1 +NC_000011.9 chr11 +NC_000021.8 chr21 +GL949748.1 HSCHR19LRC_LRC_I_CTG1 +11 NC_000011.9 +HG1591_PATCH NW_004775433.1 +GL949750.1 HSCHR19LRC_LRC_S_CTG1 +HG544_PATCH NW_003315932.1 +GL000250.1 NT_167244.1 +HG999_2_PATCH NW_003315904.1 +HG1488_PATCH NW_004070875.1 +HG1479_PATCH JH806580.1 +14 CM000676.1 +GL582966.2 NW_003571033.2 +GL000214.1 NT_167209.1 +JH636054.1 NW_003871057.1 +HG745_PATCH NW_003315948.2 +GL383572.1 NW_003315961.1 +GL000244.1 NT_167238.1 +GL000256.1 NT_167249.1 +CM000674.1 NC_000012.11 +GL383548.1 HG996_PATCH +HSCHR6_1_CTG5 NW_003315921.1 +HG1074_PATCH NW_004504302.1 +GL383579.1 HSCHR21_2_CTG1_1 +CM000686.1 chrY +GL000256.1 HSCHR6_MHC_SSTO_CTG1 +HG414_PATCH JH159143.1 +KB663609.1 NW_004504305.1 +JH591181.2 NW_003871068.1 +GL383556.1 HSCHR16_1_CTG3_1 +GL383524.1 HG280_PATCH +8 NC_000008.10 +HG871_PATCH NW_003871071.1 +HG1287_PATCH JH636052.4 +GL383523.1 HG186_PATCH +HSCHR19LRC_LRC_I_CTG1 NW_003571056.1 +JH806579.1 NW_004070869.1 +KE332502.1 NW_004775433.1 +JH806600.2 NW_004070890.2 +5 CM000667.1 +GL949748.1 NW_003571056.1 +GL383563.2 HSCHR17_1_CTG1 +GL383529.1 HSCHR4_2_CTG9 +HG987_PATCH NW_003315950.2 +CM000663.1 chr1 +GL877871.1 HG686_PATCH +HG1500_PATCH JH806577.1 +GL000220.1 NT_167214.1 +GL582979.2 HG506_HG507_HG1000_PATCH +HG1592_PATCH NW_004166863.1 +GL383582.2 NW_003315971.2 +CM000665.1 NC_000003.11 +JH806599.1 NW_004070889.1 +HG1462_PATCH NW_004070891.1 +HG29_PATCH NW_004166866.1 +GL000228.1 NT_167222.1 +GL000252.1 HSCHR6_MHC_DBB_CTG1 +HG1293_PATCH JH636054.1 +HG1441_PATCH JH806595.1 +HSCHR9_1_CTG1 NW_003315928.1 +HG1440_PATCH JH806594.1 +HG971_PATCH NW_003871084.1 +JH806575.1 NW_004070865.1 +GL383554.1 HSCHR15_1_CTG4 +JH159144.1 NW_003871088.1 +GL383516.1 NW_003315903.1 +22 CM000684.1 +HG686_PATCH NW_003571032.1 +HG27_PATCH JH806576.1 +HSCHR18_1_CTG2_1 NW_003315958.1 +HG1079_PATCH NW_004166865.1 +JH636057.1 NW_003871063.1 +17 CM000679.1 +GL383559.2 HG745_PATCH +GL383532.1 NW_003315920.1 +JH806583.1 NW_004070873.1 +JH159142.2 NW_003871080.1 +GL383549.1 NW_003315938.1 +HSCHR19_3_CTG3 NW_003315965.1 +GL383578.1 NW_003315967.1 +10 chr10 +GL383528.1 NW_003315915.1 +GL582977.2 NW_003571053.2 +16 CM000678.1 +HSCHR17_5_CTG4 NW_003871092.1 +GL000253.1 NT_167246.1 +GL000232.1 NT_167226.1 +GL949744.1 NW_003571046.1 +HG174_HG254_PATCH KE332496.1 +GL383552.1 NW_003315941.1 +HSCHR21_4_CTG1_1 NW_003315970.1 +HG104_HG975_PATCH NW_003315923.1 +JH159147.1 NW_003871092.1 +GL383567.1 HSCHR18_1_CTG1_1 +JH806574.2 NW_004070864.2 +19 CM000681.1 +HSCHR17_5_CTG4 JH159147.1 +HSCHR4_2_CTG9 NW_003315916.1 +HG280_PATCH NW_003315911.1 +GL383548.1 NW_003315937.1 +13 CM000675.1 +JH159138.1 NW_003871076.1 +GL582975.1 NW_003571051.1 +HSCHR17_1_CTG5 NT_167251.1 +GL383571.1 HSCHR18_2_CTG2 +HG1133_PATCH NW_003571047.1 +X chrX +HG418_PATCH NW_003871066.2 +GL383545.1 HSCHR10_1_CTG2 +HSCHR2_2_CTG12 NW_003571033.2 +HG50_PATCH KB663605.1 +HG1490_PATCH JH806603.1 +GL383550.1 HSCHR12_1_CTG2_1 +GL383564.1 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NW_003315955.1 +7 NC_000007.13 +HSCHR19LRC_COX2_CTG1 NW_003571055.1 +JH159146.1 NW_003871091.1 +HG243_PATCH NW_003315924.1 +GL383533.1 HSCHR6_1_CTG5 +HG991_PATCH NW_003315912.1 +HG1082_HG167_PATCH NW_004775428.1 +GL383525.1 NW_003315912.1 +GL383565.1 NW_003315954.1 +NC_000023.10 X +HG306_PATCH NW_003871078.1 +CM000684.1 chr22 +GL000247.1 NT_167241.1 +HG871_PATCH JH636060.1 +KE332496.1 NW_004775427.1 +HG1063_PATCH JH159133.1 +JH806587.1 NW_004070877.1 +KE332497.1 NW_004775428.1 +NC_000017.10 chr17 +HG1459_PATCH JH806600.2 +GL383541.1 HSCHR9_2_CTG35 +HG957_PATCH KE332495.1 +GL000217.1 NT_167212.1 +HG75_PATCH NW_003315949.1 +GL383545.1 NW_003315934.1 +HG1292_PATCH NW_003871056.3 +GL000227.1 NT_167221.1 +HSCHR16_1_CTG3_1 NW_003315945.1 +NC_000003.11 chr3 +GL383539.1 NW_003315928.1 +KB021644.1 NW_004166862.1 +6 chr6 +GL877876.1 NW_003571050.1 +14 chr14 +HG1473_PATCH JH806575.1 +NC_000020.10 chr20 +JH591183.1 NW_003871070.1 +HG729_PATCH NW_003871094.1 +GL383532.1 HSCHR5_2_CTG1 +9 chr9 +GL383517.1 HG999_2_PATCH +GL000239.1 NT_167233.1 +CM000678.1 NC_000016.9 +JH159143.1 NW_003871081.1 +GL383550.1 NW_003315939.1 +GL000210.1 NT_113950.2 +HSCHR17_4_CTG4 JH159146.1 +GL000255.1 HSCHR6_MHC_QBL_CTG1 +GL383567.1 NW_003315956.1 +GL949750.1 NW_003571058.1 +GL877875.1 NW_003571049.1 +GL000208.1 NT_113948.1 +HG1287_PATCH NW_003871055.3 +GL582972.1 HG946_PATCH +GL383521.1 HSCHR2_1_CTG1 +HSCHR5_3_CTG1 NW_003571036.1 +HSCHR10_1_CTG2 NW_003315934.1 +GL000191.1 NT_113878.1 +GL582968.1 HG115_PATCH +HSCHR2_1_CTG12 NW_003315909.1 +NC_000005.9 chr5 +HG1007_PATCH NW_003571031.1 +HG388_HG400_PATCH JH159142.2 +CM000674.1 chr12 +GL383551.1 HSCHR12_1_CTG5 +KB021648.1 NW_004166866.1 +GL000230.1 NT_167224.1 +HG357_PATCH KB663604.1 +CM000680.1 chr18 +HG1443_HG1444_PATCH JH806597.1 +HSCHR12_1_CTG5 NW_003315940.1 +HG1487_PATCH JH806584.1 +JH159141.2 NW_003871079.1 +HSCHR19LRC_LRC_S_CTG1 NW_003571058.1 +CM000672.1 chr10 +HG1439_PATCH JH806593.1 +GL949741.1 NW_003571030.1 +GL383519.1 HSCHR1_2_CTG31 +HSCHR19LRC_LRC_J_CTG1 NW_003571057.1 +CM000675.1 NC_000013.10 +20 NC_000020.10 +21 chr21 +GL000246.1 NT_167240.1 +8 CM000670.1 +GL383529.1 NW_003315916.1 +HSCHR20_1_CTG1 NW_003315966.1 +CM000685.1 NC_000023.10 +HSCHR6_MHC_MCF_CTG1 NT_167247.1 +HG1435_PATCH JH806589.1 +HG998_2_PATCH NW_003315927.1 +21 CM000683.1 +GL383531.1 HSCHR5_1_CTG5 +12 chr12 +JH591182.1 NW_003871069.1 +NC_000006.11 chr6 +HSCHR21_1_CTG1_1 NW_003315967.1 +GL383566.1 HSCHR17_3_CTG4 +GL383523.1 NW_003315910.1 +3 CM000665.1 +HG329_PATCH JH720449.1 +JH806581.1 NW_004070871.1 +GL949749.1 NW_003571057.1 +HG957_PATCH NW_004775426.1 +HG329_PATCH NW_003871096.1 +HG142_HG150_NOVEL_TEST JH159136.1 +GL339450.1 HG79_PATCH +GL339449.2 NW_003315917.2 +GL000225.1 NT_167219.1 +HG706_PATCH NW_003571035.1 +CM000664.1 NC_000002.11 +HSCHR1_1_CTG31 NW_003315905.1 +HG1082_HG167_PATCH KE332497.1 +GL383570.1 HSCHR18_2_CTG1_1 +JH720451.1 NW_003871098.1 +GL383536.1 HG243_PATCH +HG1350_HG959_PATCH KE332505.1 +CM000664.1 chr2 +HG1433_PATCH JH806587.1 +NC_000002.11 chr2 +GL383528.1 HSCHR4_1_CTG6 +HG1502_PATCH NW_004070869.1 +HG193_PATCH NW_004775429.1 +HG946_PATCH NW_003571041.1 +JH159134.2 NW_003871064.1 +GL949753.1 NW_003571061.1 +HSCHR12_1_CTG2 NW_003315938.1 +HG953_PATCH NW_004504299.1 +CM000666.1 chr4 +HG183_PATCH NW_003315947.1 +CM000672.1 NC_000010.10 +GL949747.1 HSCHR19LRC_COX2_CTG1 +GL383577.1 NW_003315966.1 +HG305_PATCH JH159139.1 +HG1473_PATCH NW_004070865.1 +NC_000001.10 chr1 +GL000207.1 NT_113947.1 +GL000215.1 NT_167210.1 +GL383531.1 NW_003315919.1 +HG122_PATCH JH720443.2 +HG1592_PATCH KB021645.1 +HG271_PATCH NW_003871087.1 +GL949752.1 NW_003571060.1 +JH159132.1 NW_003871059.1 +GL000226.1 NT_167220.1 +HG1497_PATCH JH159150.3 +HSCHR17_6_CTG4 JH159148.1 +NC_000018.9 chr18 +HG883_PATCH NW_003871090.1 +NC_000010.10 chr10 +JH720444.2 NW_003871083.2 +JH159136.1 NW_003871073.1 diff --git a/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/info.txt b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/info.txt new file mode 100644 index 000000000..e5f90b671 --- /dev/null +++ b/.tests/test-workflow/resources/cache/vep/homo_sapiens/102_GRCh37/info.txt @@ -0,0 +1,21 @@ +species homo_sapiens +assembly GRCh37 +sift b +polyphen b +source_sift sift5.2.2 +source_gencode GENCODE 19 +source_polyphen 2.2.2 +source_assembly GRCh37.p13 +source_genebuild 2011-04 +variation_cols chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,clin_sig_allele,pubmed,var_synonyms,AFR,AMR,EAS,EUR,SAS,AA,EA,gnomAD,gnomAD_AFR,gnomAD_AMR,gnomAD_ASJ,gnomAD_EAS,gnomAD_FIN,gnomAD_NFE,gnomAD_OTH,gnomAD_SAS +source_HGMD-PUBLIC 20194 +source_ESP 20141103 +source_COSMIC 90 +source_ClinVar 201912 +source_dbSNP 153 +source_1000genomes phase3 +source_gnomAD r2.1 +var_type tabix +regulatory 1 +cell_types A549,A673,B,B_(PB),CD14+_monocyte_(PB),CD14+_monocyte_1,CD4+_CD25+_ab_Treg_(PB),CD4+_ab_T,CD4+_ab_T_(PB)_1,CD4+_ab_T_(PB)_2,CD4+_ab_T_(Th),CD8+_ab_T_(CB),CD8+_ab_T_(PB),CMP_CD4+_1,CMP_CD4+_2,CMP_CD4+_3,CM_CD4+_ab_T_(VB),DND-41,EB_(CB),EM_CD4+_ab_T_(PB),EM_CD8+_ab_T_(VB),EPC_(VB),GM12878,H1-hESC_2,H1-hESC_3,H9_1,HCT116,HSMM,HUES48,HUES6,HUES64,HUVEC,HUVEC-prol_(CB),HeLa-S3,HepG2,K562,M0_(CB),M0_(VB),M1_(CB),M1_(VB),M2_(CB),M2_(VB),MCF-7,MM.1S,MSC,MSC_(VB),NHLF,NK_(PB),NPC_1,NPC_2,PC-3,PC-9,SK-N.,T_(PB),Th17,UCSF-4,adrenal_gland,aorta,astrocyte,bipolar_neuron,brain_1,brain_2,cardiac_muscle,dermal_fibroblast,endocrine_pancreas,endodermal,eosinophil_(VB),esophagus,foreskin_fibroblast_1,foreskin_fibroblast_2,foreskin_keratinocyte_2,foreskin_melanocyte_1,foreskin_melanocyte_2,germinal_matrix,heart,hepatocyte,iPS-15b,iPS-20b,iPS_DF_19.11,iPS_DF_6.9,keratinocyte,kidney,large_intestine,left_ventricle,leg_muscle,lung_1,lung_2,mammary_epithelial_1,mammary_epithelial_2,monocyte_(CB),monocyte_(VB),myotube,naive_B_(VB),neuron,neurosphere_(C),neurosphere_(GE),neutro_myelocyte,neutrophil_(CB),neutrophil_(VB),osteoblast,ovary,pancreas,placenta,psoas_muscle,right_atrium,right_ventricle,sigmoid_colon,small_intestine_1,small_intestine_2,spleen,stomach_1,stomach_2,thymus_1,thymus_2,trophoblast,trunk_muscle +source_regbuild 1.0 diff --git a/.tests/test-workflow/workflow/Snakefile b/.tests/test-workflow/workflow/Snakefile new file mode 100644 index 000000000..f0a55fa3d --- /dev/null +++ b/.tests/test-workflow/workflow/Snakefile @@ -0,0 +1,36 @@ +from snakemake.utils import validate + + +configfile: "config/config.yaml" + + +validate(config, "schemas/config.schema.yaml") + + +include: "rules/common.smk" +include: "rules/reference.smk" +include: "rules/stats.smk" +include: "rules/cancer_wes.smk" + + +rule all: + input: + expand( + "pipelines/snappy-cancer_wes/{step_name}/output/{mapper}.{caller}.{annotator}.filtered.{sample}/out/{mapper}.{caller}.{annotator}.filtered.{sample}.vcf.gz", + step_name=["somatic_variant_filtration"], + sample=["case001subregion-T1-DNA1-WES1"], + mapper=["bwa"], + caller=["mutect2"], + annotator=["vep"], + ), + + +rule generate_snakemake_profile_config: + output: + config="profile/snakemake/config.yaml", + conda: + "envs/base.yaml" + log: + "logs/generate_snakemake_profile_config", + shell: + """echo "use-conda: true\nconda-frontend: mamba\ncores: all" > {output.config} 2> {log}""" diff --git a/.tests/test-workflow/workflow/envs/base.yaml b/.tests/test-workflow/workflow/envs/base.yaml new file mode 100644 index 000000000..5fab88400 --- /dev/null +++ b/.tests/test-workflow/workflow/envs/base.yaml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bash ==5.2.21 \ No newline at end of file diff --git a/.tests/test-workflow/workflow/envs/bioawk.yaml b/.tests/test-workflow/workflow/envs/bioawk.yaml new file mode 100644 index 000000000..d15f0df20 --- /dev/null +++ b/.tests/test-workflow/workflow/envs/bioawk.yaml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioawk ==1.0 \ No newline at end of file diff --git a/.tests/test-workflow/workflow/envs/samtools.yaml b/.tests/test-workflow/workflow/envs/samtools.yaml new file mode 100644 index 000000000..c460fe489 --- /dev/null +++ b/.tests/test-workflow/workflow/envs/samtools.yaml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - samtools ==1.18 \ No newline at end of file diff --git a/.tests/test-workflow/workflow/envs/snappy.post-deploy.sh b/.tests/test-workflow/workflow/envs/snappy.post-deploy.sh new file mode 100644 index 000000000..6c23d6f01 --- /dev/null +++ b/.tests/test-workflow/workflow/envs/snappy.post-deploy.sh @@ -0,0 +1,15 @@ +#!env bash +set -o pipefail +conda init +conda activate "$CONDA_PREFIX" + +if [[ -n "${GITHUB_WORKSPACE}" ]]; then + cd "${GITHUB_WORKSPACE}" || exit +else + if [[ -d /github/workspace ]]; then + cd /github/workspace/ || exit + else + cd snappy-pipeline || exit + fi +fi +pip install -e . diff --git a/.tests/test-workflow/workflow/envs/snappy.yaml b/.tests/test-workflow/workflow/envs/snappy.yaml new file mode 100644 index 000000000..d095ae02c --- /dev/null +++ b/.tests/test-workflow/workflow/envs/snappy.yaml @@ -0,0 +1,74 @@ +channels: + - conda-forge + - bioconda +dependencies: + + # Fundamentals + - python >=3.11.0 + - pip =24 + - git-lfs =3.5 + - gcc_linux-64 =13.2 + - gxx_linux-64 =13.2 + + # basics some snappy wrappers rely on + - coreutils =9.5 + - gawk =5.3 + - bash =5.2 + - gzip =1.13 + + # Snakemake is used for providing the actual wrapper calling functionality + - snakemake >=7,<8 + + # Additional libraries used by snappy + - ruamel.yaml =0.18 # Nice, round-trip enabled YAML parsing + - fasteners =0.17 # File-based locks + - termcolor =2.4 # Helpful for CLIs + - matplotlib =3.8 # Required for plotting + - jinja2 =3.1 # Jinja 2 template rendering + + # Bioinformatics-related libraries used by snappy + - htslib >=1.19 + - bcftools >=1.19 + - samtools >=1.19 + # both vcfpy and pysam are only used in wrappers -- and tools, which should probably be wrappers in their own regard? + # current versions compatible with py>=3.11 aren't yet available from bioconda, so install via pip instead + # - vcfpy >=0.13.8 # Library for working with VCF files + # - pysam # Support for vcfpy + # pytabix seems not to be used anywhere (and hasn't been updated in 9 years) + # nvm, it does see use in wrappers/vcfpy/add_bed/wrapper.py and wrappers/vcf_sv_filter/vcf_sv_filter.py + # - pytabix =0.1 + + # Parsing of ISA-tab + - altamisa =0.2.9 + + # miscellaneous + - attrs =23.2 + + # Dependencies for testing + - pytest-sugar =1 + - pytest =8.1 + - pytest-cov =5.0 + - coverage =7.4 + - pytest-mock =3.14 + - pytest-subprocess = 1.5 + - pyfakefs =5.4 + - snakefmt =0.10 + - ruff =0.3 + - coveralls =1.8 + + # Dependencies for documentation + - sphinx =7 + - sphinx_rtd_theme =2 + - sphinx-mdinclude =0.5 + + # CUBI libraries required by snappy (installed through pip) + - pip: + - varfish-cli >=0.6.3 + # We're trying to keep the PyPi package up to date, you might have to install + # from source, though. + # - biomedsheets >=0.11.7 + # … which is what we do here: + - git+https://github.com/bihealth/biomedsheets.git@a355c396b6e6b2f52f96f73d58cd26c3f1f5e18c + - pysam >=0.22 + - vcfpy >=0.13.8 + - pytabix diff --git a/.tests/test-workflow/workflow/rules/cancer_wes.smk b/.tests/test-workflow/workflow/rules/cancer_wes.smk new file mode 100644 index 000000000..b4c0cd6e0 --- /dev/null +++ b/.tests/test-workflow/workflow/rules/cancer_wes.smk @@ -0,0 +1,74 @@ +from textwrap import dedent +import os + + +# We could probably use relative paths in the snappy-pipeline config. +# However, we render the config file using absolute paths here, +# ensuring any missing input file is generated by this snakemake workflow here. +rule render_cancer_wes_config: + input: + template="config/cancer_wes/config.yaml.jinja2", + reference="resources/refs/subregion.fa", + bwa_index="resources/refs/subregion.bwt", + vep_cache="resources/cache/vep", + output: + config["pipeline-configuration"]["cancer_wes"]["config"], + log: + "logs/jinja/render_cancer_wes_config.log", + params: + reference=lambda wildcards, input: os.path.abspath(input.reference), + bwa_index=lambda wildcards, input: os.path.splitext(os.path.abspath(input.bwa_index))[0], + vep_cache=lambda wildcards, input: os.path.abspath(input.vep_cache), + template_engine: + "jinja2" + + +# Calls the actual snappy-pipeline instance by doing each step one-by-one in the respective step's folder +# The input files listed here are mostly hidden requirements of some steps/wrappers used in the pipeline made visible +# The output `expand(…)` call isn't strictly necessary, as for this test we are only interested in one sample +# at the moment, but that may change in the future. Also is a bit more explicit about which tools are used. +rule cancer_wes_execute_pipeline: + input: + config=config["pipeline-configuration"]["cancer_wes"]["config"], + reference="resources/refs/subregion.fa", + reference_list="resources/refs/subregion.fa.genome", + # required by the mutect2 wrapper + reference_dict="resources/refs/subregion.dict", + bwa_index="resources/refs/subregion.bwt", + snakemake_profile="profile/snakemake/config.yaml", + output: + expand( + "{dir}/{step_name}/output/{mapper}.{caller}.{annotator}.filtered.{sample}/out/{mapper}.{caller}.{annotator}.filtered.{sample}.vcf.gz", + dir=[config["pipeline-configuration"]["cancer_wes"]["workdir"]], + step_name=["somatic_variant_filtration"], + sample=["case001subregion-T1-DNA1-WES1"], + mapper=["bwa"], + caller=["mutect2"], + annotator=["vep"], + ), + params: + steps=[ + "ngs_mapping", + "somatic_variant_calling", + "somatic_variant_annotation", + "somatic_variant_filtration", + ], + profile_dir=lambda wildcards, input: os.path.abspath( + os.path.dirname(input.snakemake_profile) + ), + work_dir=lambda w, input: config["pipeline-configuration"]["cancer_wes"]["workdir"], + log: + "logs/execute-pipeline/cancer_wes.log", + conda: + "../envs/snappy.yaml" + shell: + """ + unset SNAKEMAKE_PROFILE + touch {log} + for step in {params.steps} + do + pushd {params.work_dir}/${{step}} || exit + snappy-snake --snappy-pipeline-use-profile {params.profile_dir} || exit + popd + done + """ diff --git a/.tests/test-workflow/workflow/rules/common.smk b/.tests/test-workflow/workflow/rules/common.smk new file mode 100644 index 000000000..3edea7a00 --- /dev/null +++ b/.tests/test-workflow/workflow/rules/common.smk @@ -0,0 +1,40 @@ +from functools import cache + +import pandas as pd + + +@cache +def samplesheet(pipeline: str) -> pd.DataFrame: + return pd.read_csv( + config["pipeline-configuration"][pipeline]["samplesheet"], + sep="\t", + comment="#", + skiprows=12, + ) + + +def samples(pipeline: str) -> list[str]: + return list(samplesheet(pipeline)["sampleName"].unique()) + + +def folder_names(pipeline: str) -> list[str]: + return list(samplesheet(pipeline)["folderName"].unique()) + + +def reference_path() -> str: + if chrom := config["reference"].get("chromosome", None): + return f"resources/refs/{chrom}.fa.gz" + else: + return "resources/refs/genome.fa.gz" + + +def reference_faidx_region_string(wildcards) -> str: + chrom = config["reference"].get("chromosome", None) + region = config["reference"].get("region", None) + match chrom, region: + case None, None: + return f"" + case chrom, None: + return f"{chrom}" + case chrom, region: + return f"{chrom}:{region}" diff --git a/.tests/test-workflow/workflow/rules/reference.smk b/.tests/test-workflow/workflow/rules/reference.smk new file mode 100644 index 000000000..bf531e3dc --- /dev/null +++ b/.tests/test-workflow/workflow/rules/reference.smk @@ -0,0 +1,98 @@ +rule get_single_chromosome: + output: + reference_path(), + params: + species=config["reference"].get("species", "homo_sapiens"), + datatype=config["reference"].get("datatype", "dna"), + build=config["reference"].get("build", "GRCh37"), + release=config["reference"].get("release", 111), + chromosome=[config["reference"].get("chromosome", "12")], + log: + "logs/get_genome.log", + # cache: "omit-software" + wrapper: + "v3.5.3/bio/reference/ensembl-sequence" + + +rule bgzip: + input: + "{prefix}", + output: + "{prefix}.gz", + params: + extra="", # optional + threads: 1 + log: + "logs/bgzip/{prefix}.log", + wrapper: + "v3.5.3/bio/bgzip" + + +rule samtools_index: + input: + "{sample}", + output: + "{sample}.fai", + log: + "logs/samtools_index/{sample}.log", + params: + extra="", # optional params string + wrapper: + "v3.5.3/bio/samtools/faidx" + + +# restrict the reference to a small region on chr12 containing KRAS +rule reference_subregion: + input: + reference_path(), + output: + "resources/refs/subregion.fa", + log: + "logs/restrict_reference.log", + # cache: "omit-software" + params: + region=reference_faidx_region_string, + conda: + "../envs/samtools.yaml" + shell: + "samtools faidx {input} {params.region} > {output} 2> {log}" + + +rule contig_list: + input: + "{reference}.fa", + output: + "{reference}.fa.genome", + conda: + "../envs/bioawk.yaml" + log: + "logs/{reference}.contig_list.log", + shell: + "bioawk -c fastx '{{print $name;}}' {input} > {output} 2> {log}" + + +rule samtools_dict: + input: + "{reference}.fa", + output: + "{reference}.dict", + conda: + "../envs/samtools.yaml" + log: + "logs/{reference}.samtools_dict.log", + shell: + "samtools dict {input} > {output} 2> {log}" + + +rule bwa_index: + input: + "{genome}.fa", + output: + idx=multiext("{genome}", ".amb", ".ann", ".bwt", ".pac", ".sa"), + log: + "logs/bwa_index/{genome}.log", + params: + extra="", + # cache: "omit-software" + wrapper: + "v3.5.3/bio/bwa/index" diff --git a/.tests/test-workflow/workflow/rules/stats.smk b/.tests/test-workflow/workflow/rules/stats.smk new file mode 100644 index 000000000..ea18832f0 --- /dev/null +++ b/.tests/test-workflow/workflow/rules/stats.smk @@ -0,0 +1,12 @@ +rule count_alignments: + input: + bam="{file}.bam", + output: + counts="{file}.alignment_counts.txt", + threads: workflow.cores + log: + "logs/count_alignments/{file}.log", + conda: + "../envs/samtools.yaml" + shell: + """samtools view -@{threads} -c {input.bam} > {output.counts} 2> {log}""" diff --git a/.tests/test-workflow/workflow/schemas/config.schema.yaml b/.tests/test-workflow/workflow/schemas/config.schema.yaml new file mode 100644 index 000000000..e72bb9acc --- /dev/null +++ b/.tests/test-workflow/workflow/schemas/config.schema.yaml @@ -0,0 +1,55 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" + +description: configuration file for snappy-end-to-end workflow + +type: object + +definitions: + pipeline-entry: + type: object + properties: + workdir: + type: string + config: + type: string + samplesheet: + type: string + required: + - workdir + - config + - samplesheet + +properties: + reference: + type: object + properties: + species: + type: string + description: reference species, e.g. "homo_sapiens" + datatype: + type: string + enum: ["dna", "rna"] + build: + type: string + release: + type: integer + minimum: 0 + chromosome: + type: string + region: + type: string + required: + - species + - datatype + - build + - release + + pipeline-configuration: + type: object + additionalProperties: + $ref: "#/definitions/pipeline-entry" + + +required: + - reference + - pipeline-configuration \ No newline at end of file