diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c0e32dfed..f2ff33e4d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -133,7 +133,6 @@ jobs: - name: Test rule ${{ matrix.rule }} on ${{ matrix.technology }} ${{ matrix.seq_method }} data uses: snakemake/snakemake-github-action@v1.24.0 with: - stagein: mamba env create -f workflow/envs/trinity.yaml -n trinity directory: .tests snakefile: workflow/Snakefile args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}" diff --git a/workflow/envs/abyss.yaml b/workflow/envs/abyss.yaml index d108c4bbe..d78e585d5 100644 --- a/workflow/envs/abyss.yaml +++ b/workflow/envs/abyss.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - abyss =2.3.1 diff --git a/workflow/envs/bamclipper.yaml b/workflow/envs/bamclipper.yaml index 403412f2b..bffea9bdf 100644 --- a/workflow/envs/bamclipper.yaml +++ b/workflow/envs/bamclipper.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - bamclipper =1.0 - samtools =1.14 # see https://github.com/merenlab/anvio/issues/1479 diff --git a/workflow/envs/bcftools.yaml b/workflow/envs/bcftools.yaml index 22df755f9..af0652bb7 100644 --- a/workflow/envs/bcftools.yaml +++ b/workflow/envs/bcftools.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - bcftools =1.10 diff --git a/workflow/envs/bedtools.yaml b/workflow/envs/bedtools.yaml index 9a8a4f74c..3df68a030 100644 --- a/workflow/envs/bedtools.yaml +++ b/workflow/envs/bedtools.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - bedtools =2.30.0 diff --git a/workflow/envs/canu.yaml b/workflow/envs/canu.yaml index a8fec4951..c181758e3 100644 --- a/workflow/envs/canu.yaml +++ b/workflow/envs/canu.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: # do not use canu 2.2 ! - canu =2.1.1 diff --git a/workflow/envs/delly.yaml b/workflow/envs/delly.yaml index 5e84c3e7e..0915d03b6 100644 --- a/workflow/envs/delly.yaml +++ b/workflow/envs/delly.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - delly =0.8.7 - pysam =0.16 diff --git a/workflow/envs/entrez.yaml b/workflow/envs/entrez.yaml index 3387557de..8378303d8 100644 --- a/workflow/envs/entrez.yaml +++ b/workflow/envs/entrez.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - - entrez-direct =13.9 + - entrez-direct =16.2 diff --git a/workflow/envs/fgbio.yaml b/workflow/envs/fgbio.yaml index 14ee90356..51f5e3524 100644 --- a/workflow/envs/fgbio.yaml +++ b/workflow/envs/fgbio.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - fgbio =1.3 diff --git a/workflow/envs/genometools.yaml b/workflow/envs/genometools.yaml index 8b295f90f..975fd5b6c 100644 --- a/workflow/envs/genometools.yaml +++ b/workflow/envs/genometools.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - genometools-genometools =1.6.2 diff --git a/workflow/envs/gff3sort.yaml b/workflow/envs/gff3sort.yaml index c3a285ae4..d554c69ff 100644 --- a/workflow/envs/gff3sort.yaml +++ b/workflow/envs/gff3sort.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - gff3sort = 0.1 diff --git a/workflow/envs/kraken.yaml b/workflow/envs/kraken.yaml index 1e279c562..979d75cff 100644 --- a/workflow/envs/kraken.yaml +++ b/workflow/envs/kraken.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - kraken2 =2.1.1 - krona =2.7.1 diff --git a/workflow/envs/longshot.yaml b/workflow/envs/longshot.yaml index e9874cc14..244a10869 100644 --- a/workflow/envs/longshot.yaml +++ b/workflow/envs/longshot.yaml @@ -1,4 +1,6 @@ channels: + - conda-forge - bioconda + - nodefaults dependencies: - longshot =0.4 diff --git a/workflow/envs/mason.yaml b/workflow/envs/mason.yaml index cd253e39e..5025c1576 100644 --- a/workflow/envs/mason.yaml +++ b/workflow/envs/mason.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - mason =2.0 diff --git a/workflow/envs/medaka.yaml b/workflow/envs/medaka.yaml index 591aae2cb..dc5efb316 100644 --- a/workflow/envs/medaka.yaml +++ b/workflow/envs/medaka.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - medaka =1.0 - tensorflow =1.14 diff --git a/workflow/envs/megahit.yaml b/workflow/envs/megahit.yaml index 19b84287a..278221b32 100644 --- a/workflow/envs/megahit.yaml +++ b/workflow/envs/megahit.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - megahit =1.2 diff --git a/workflow/envs/minimap2.yaml b/workflow/envs/minimap2.yaml index a44e24867..b8696b0df 100644 --- a/workflow/envs/minimap2.yaml +++ b/workflow/envs/minimap2.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - minimap2 =2.22 diff --git a/workflow/envs/multiqc.yaml b/workflow/envs/multiqc.yaml index e01cee038..990cfe07c 100644 --- a/workflow/envs/multiqc.yaml +++ b/workflow/envs/multiqc.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - multiqc =1.11 diff --git a/workflow/envs/nanofilt.yaml b/workflow/envs/nanofilt.yaml index e845b6fba..5c556e2c4 100644 --- a/workflow/envs/nanofilt.yaml +++ b/workflow/envs/nanofilt.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - nanofilt =2.8 - gzip =1.11 diff --git a/workflow/envs/nanoqc.yaml b/workflow/envs/nanoqc.yaml index 24ef61680..a772998c8 100644 --- a/workflow/envs/nanoqc.yaml +++ b/workflow/envs/nanoqc.yaml @@ -1,4 +1,6 @@ channels: + - conda-forge - bioconda + - nodefaults dependencies: - nanoqc =0.9 diff --git a/workflow/envs/notramp.yaml b/workflow/envs/notramp.yaml index 2a57c7ba6..4f35530d1 100644 --- a/workflow/envs/notramp.yaml +++ b/workflow/envs/notramp.yaml @@ -1,7 +1,8 @@ channels: - simakro - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - notramp =1.0.5 - minimap2 =2.22 diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index 4cbee4451..52f9310fd 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -1,5 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - pangolin =4.1.2 + - tabulate <0.9 # TODO remove once pangolin 4.1.3 is available in bioconda diff --git a/workflow/envs/pysam.yaml b/workflow/envs/pysam.yaml index 125149cd4..2b748a104 100644 --- a/workflow/envs/pysam.yaml +++ b/workflow/envs/pysam.yaml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + - nodefaults dependencies: - jupyter =1.0 - pysam =0.16 diff --git a/workflow/envs/python.yaml b/workflow/envs/python.yaml index 15b460ad8..d918d4686 100644 --- a/workflow/envs/python.yaml +++ b/workflow/envs/python.yaml @@ -2,6 +2,7 @@ channels: - conda-forge - bioconda - anaconda + - nodefaults dependencies: - pandas =1.2 - jupyter =1.0 diff --git a/workflow/envs/quast.yaml b/workflow/envs/quast.yaml index fd77ea287..3f361e8a3 100644 --- a/workflow/envs/quast.yaml +++ b/workflow/envs/quast.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - quast =5.0 diff --git a/workflow/envs/ragoo.yaml b/workflow/envs/ragoo.yaml index 19ba3af9b..3e3edfcd9 100644 --- a/workflow/envs/ragoo.yaml +++ b/workflow/envs/ragoo.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda - imperial-college-research-computing + - nodefaults dependencies: - ragoo =1.1 diff --git a/workflow/envs/rbt.yaml b/workflow/envs/rbt.yaml index c02a4aa57..b587821b4 100644 --- a/workflow/envs/rbt.yaml +++ b/workflow/envs/rbt.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - rust-bio-tools =0.39 diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml index 8de8caf4e..5c86db4c8 100644 --- a/workflow/envs/samtools.yaml +++ b/workflow/envs/samtools.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - samtools =1.14 diff --git a/workflow/envs/seqtk.yaml b/workflow/envs/seqtk.yaml index 101cc3c9d..3db1b1995 100644 --- a/workflow/envs/seqtk.yaml +++ b/workflow/envs/seqtk.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - seqtk =1.3 diff --git a/workflow/envs/snakemake.yaml b/workflow/envs/snakemake.yaml index 522c65b4d..bf82582ac 100644 --- a/workflow/envs/snakemake.yaml +++ b/workflow/envs/snakemake.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - snakemake =7.0 diff --git a/workflow/envs/sourmash.yaml b/workflow/envs/sourmash.yaml index f24fcfd79..8182f7cea 100644 --- a/workflow/envs/sourmash.yaml +++ b/workflow/envs/sourmash.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - sourmash =3.5 diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml index 4e37a04a2..d88fde2cb 100644 --- a/workflow/envs/spades.yaml +++ b/workflow/envs/spades.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - spades =3.15 diff --git a/workflow/envs/svn.yaml b/workflow/envs/svn.yaml index 19014f0ed..f803222eb 100644 --- a/workflow/envs/svn.yaml +++ b/workflow/envs/svn.yaml @@ -1,4 +1,5 @@ channels: - anaconda + - nodefaults dependencies: - svn =1.10 diff --git a/workflow/envs/tabix.yaml b/workflow/envs/tabix.yaml index 6db26455c..7fa9caf2c 100644 --- a/workflow/envs/tabix.yaml +++ b/workflow/envs/tabix.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - tabix =0.2 - curl diff --git a/workflow/envs/trinity.yaml b/workflow/envs/trinity.yaml index 90993fc33..8476259a8 100644 --- a/workflow/envs/trinity.yaml +++ b/workflow/envs/trinity.yaml @@ -1,7 +1,7 @@ channels: - - bioconda - conda-forge - - defaults + - bioconda + - nodefaults dependencies: - trinity =2.13 # ensure that we use a bowtie2 that already contains fixed dependency constraints diff --git a/workflow/envs/ucsc.yaml b/workflow/envs/ucsc.yaml index 46f35cd28..47e50dbbd 100644 --- a/workflow/envs/ucsc.yaml +++ b/workflow/envs/ucsc.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - ucsc-bigbedtobed =377 diff --git a/workflow/envs/unix.yaml b/workflow/envs/unix.yaml index f1899ae37..56a2099aa 100644 --- a/workflow/envs/unix.yaml +++ b/workflow/envs/unix.yaml @@ -1,6 +1,7 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - curl - sed diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml index 10b6135e9..39ff16514 100644 --- a/workflow/envs/varlociraptor.yaml +++ b/workflow/envs/varlociraptor.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - varlociraptor =4.9 diff --git a/workflow/envs/velvet.yaml b/workflow/envs/velvet.yaml index eca4e7763..6c7e886a1 100644 --- a/workflow/envs/velvet.yaml +++ b/workflow/envs/velvet.yaml @@ -1,5 +1,6 @@ channels: - - bioconda - conda-forge + - bioconda + - nodefaults dependencies: - velvet =1.2 diff --git a/workflow/notebooks/assembly-benchmark-results.py.ipynb b/workflow/notebooks/assembly-benchmark-results.py.ipynb index d8aa95695..46e7dbc64 100644 --- a/workflow/notebooks/assembly-benchmark-results.py.ipynb +++ b/workflow/notebooks/assembly-benchmark-results.py.ipynb @@ -197,5 +197,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/call-strains.py.ipynb b/workflow/notebooks/call-strains.py.ipynb index ff610b737..686f045a9 100644 --- a/workflow/notebooks/call-strains.py.ipynb +++ b/workflow/notebooks/call-strains.py.ipynb @@ -74,5 +74,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/plot-all-strains-kallisto.py.ipynb b/workflow/notebooks/plot-all-strains-kallisto.py.ipynb index abe135106..24b3e31aa 100644 --- a/workflow/notebooks/plot-all-strains-kallisto.py.ipynb +++ b/workflow/notebooks/plot-all-strains-kallisto.py.ipynb @@ -53,5 +53,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/plot-all-strains-pangolin.py.ipynb b/workflow/notebooks/plot-all-strains-pangolin.py.ipynb index 502048479..7785d2b1d 100644 --- a/workflow/notebooks/plot-all-strains-pangolin.py.ipynb +++ b/workflow/notebooks/plot-all-strains-pangolin.py.ipynb @@ -46,5 +46,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/plot-read-call.py.ipynb b/workflow/notebooks/plot-read-call.py.ipynb index aab051f9a..3ccc4d147 100644 --- a/workflow/notebooks/plot-read-call.py.ipynb +++ b/workflow/notebooks/plot-read-call.py.ipynb @@ -100,5 +100,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/plot-strains-kallisto.py.ipynb b/workflow/notebooks/plot-strains-kallisto.py.ipynb index c2a26048a..bcfede786 100644 --- a/workflow/notebooks/plot-strains-kallisto.py.ipynb +++ b/workflow/notebooks/plot-strains-kallisto.py.ipynb @@ -60,5 +60,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/notebooks/test-benchmark-results.py.ipynb b/workflow/notebooks/test-benchmark-results.py.ipynb index 038f91089..616ac7ec7 100644 --- a/workflow/notebooks/test-benchmark-results.py.ipynb +++ b/workflow/notebooks/test-benchmark-results.py.ipynb @@ -52,5 +52,5 @@ } }, "nbformat": 4, - "nbformat_minor": 4 + "nbformat_minor": 5 } diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 6400076ac..d29581213 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -386,10 +386,6 @@ def get_reference(suffix=""): return inner -def get_bwa_index_prefix(index_paths): - return os.path.splitext(index_paths[0])[0] - - def get_reads(wildcards): # alignment against the human reference genome is done with trimmed reads, # since this alignment is used to generate the ordered, non human reads diff --git a/workflow/rules/lineage_variant_calling.smk b/workflow/rules/lineage_variant_calling.smk index 3f6bbeed1..f50053f1f 100644 --- a/workflow/rules/lineage_variant_calling.smk +++ b/workflow/rules/lineage_variant_calling.smk @@ -48,6 +48,15 @@ rule generate_lineage_variant_table: "../scripts/generate-lineage-variant-table.py" +rule get_lineage_variant_table: + input: + expand( + "results/{date}/lineage-variant-report/{sample}.csv", + date="2022-05-16", + sample=get_samples_for_date("2022-05-16"), + ), + + use rule overview_table_html as generate_lineage_variant_report with: input: "results/{date}/lineage-variant-report/{sample}.csv", diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk index 5e1e26231..d45cd0a38b 100644 --- a/workflow/rules/qc.smk +++ b/workflow/rules/qc.smk @@ -13,7 +13,7 @@ rule fastqc: log: "logs/{date}/fastqc/{sample}.log", wrapper: - "0.69.0/bio/fastqc" + "v1.12.2/bio/fastqc" # TODO Change multiqc rules back to MultiQC wrapper once v1.11 is released @@ -38,13 +38,13 @@ rule multiqc: output: "results/{date}/qc/multiqc.html", params: - params=( + extra=( "--config config/multiqc_config.yaml --title 'Results for data from {date}'" ), log: "logs/{date}/multiqc.log", wrapper: - "v0.86.0/bio/multiqc" + "v1.15.1/bio/multiqc" rule multiqc_lab: @@ -66,11 +66,11 @@ rule multiqc_lab: subcategory="1. Quality Control", ), params: - params="--config config/multiqc_config_lab.yaml --title 'Results for data from {date}'", + extra="--config config/multiqc_config_lab.yaml --title 'Results for data from {date}'", log: "logs/{date}/multiqc.log", wrapper: - "v0.86.0/bio/multiqc" + "v1.15.1/bio/multiqc" rule samtools_flagstat: @@ -81,7 +81,7 @@ rule samtools_flagstat: log: "logs/{date}/samtools/{sample}_flagstat.log", wrapper: - "0.70.0/bio/samtools/flagstat" + "v1.15.1/bio/samtools/flagstat" rule samtools_depth: diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk index 8abdde7ed..8d93acc74 100644 --- a/workflow/rules/read_clipping.smk +++ b/workflow/rules/read_clipping.smk @@ -13,12 +13,11 @@ rule samtools_sort: extra=( lambda wildcards: "-n -m 4G" if wildcards.sorted_by == "name" else "-m 4G" ), - tmp_dir="/tmp/", log: "logs/{date}/sort-bam/{read_type}~{sorted_by}/{sample}.{stage}.log", threads: 8 wrapper: - "0.74.0/bio/samtools/sort" + "v1.15.1/bio/samtools/sort" rule bed_to_bedpe: diff --git a/workflow/rules/read_mapping.smk b/workflow/rules/read_mapping.smk index b4b2243b2..5c369aef5 100644 --- a/workflow/rules/read_mapping.smk +++ b/workflow/rules/read_mapping.smk @@ -8,7 +8,7 @@ rule bwa_index: input: get_reference(), output: - multiext( + idx=multiext( "results/{date}/bwa/index/ref~{reference}.fasta", ".amb", ".ann", @@ -16,19 +16,17 @@ rule bwa_index: ".pac", ".sa", ), - params: - prefix=lambda w, output: get_bwa_index_prefix(output), log: "logs/{date}/bwa-index/ref~{reference}.log", wrapper: - "0.69.0/bio/bwa/index" + "v1.15.1/bio/bwa/index" rule bwa_large_index: input: get_reference(), output: - multiext( + idx=multiext( "resources/bwa/index/ref~{reference}.fasta", ".amb", ".ann", @@ -36,12 +34,10 @@ rule bwa_large_index: ".pac", ".sa", ), - params: - prefix=lambda w, output: get_bwa_index_prefix(output), log: "logs/bwa-index/ref~{reference}.log", wrapper: - "0.69.0/bio/bwa/index" + "v1.15.1/bio/bwa/index" rule map_reads: @@ -53,27 +49,24 @@ rule map_reads: log: "logs/{date}/bwa-mem/ref~{reference}/{sample}.log", params: - index=lambda w, input: get_bwa_index_prefix(input.idx), extra="", - sort="samtools", + sorting="samtools", sort_order="coordinate", threads: 8 wrapper: - "0.69.0/bio/bwa/mem" + "v1.15.1/bio/bwa/mem" rule mark_duplicates: input: - "results/{date}/mapped/ref~{reference}/{sample}.bam", + bams="results/{date}/mapped/ref~{reference}/{sample}.bam", output: bam=temp("results/{date}/dedup/ref~{reference}/{sample}.bam"), metrics="results/{date}/qc/dedup/ref~{reference}/{sample}.metrics.txt", log: "logs/{date}/picard/dedup/ref~{reference}/{sample}.log", - params: - "", wrapper: - "0.69.0/bio/picard/markduplicates" + "v1.15.1/bio/picard/markduplicates" rule samtools_calmd: @@ -85,7 +78,7 @@ rule samtools_calmd: log: "logs/{date}/samtools-calmd/ref~{reference}/{sample}.log", params: - "-A", + extra="-A", threads: 8 wrapper: - "0.69.0/bio/samtools/calmd" + "v1.15.1/bio/samtools/calmd" diff --git a/workflow/rules/read_trimming.smk b/workflow/rules/read_trimming.smk index adad21cb0..0c1f4bdcf 100644 --- a/workflow/rules/read_trimming.smk +++ b/workflow/rules/read_trimming.smk @@ -28,7 +28,7 @@ rule fastp_pe: "logs/{date}/fastp/fastp-pe/{sample}.log", threads: 2 wrapper: - "0.70.0/bio/fastp" + "v1.15.1/bio/fastp" rule fastp_se: @@ -50,4 +50,4 @@ rule fastp_se: "results/{date}/trimmed/fastp-se/{sample}.log", threads: 2 wrapper: - "0.80.2/bio/fastp" + "v1.15.1/bio/fastp" diff --git a/workflow/rules/strain_calling.smk b/workflow/rules/strain_calling.smk index 2ace90fe7..0d86db0a5 100644 --- a/workflow/rules/strain_calling.smk +++ b/workflow/rules/strain_calling.smk @@ -37,13 +37,11 @@ rule kallisto_index: fasta="results/{date}/kallisto/strain-genomes.fasta", output: index=temp("results/{date}/kallisto/strain-genomes.idx"), - params: - extra="", log: "logs/{date}/kallisto-index.log", threads: 8 wrapper: - "0.70.0/bio/kallisto/index" + "v1.15.1/bio/kallisto/index" rule kallisto_metrics: @@ -74,7 +72,7 @@ rule kallisto_quant: "logs/{date}/kallisto_quant/{sample}.log", threads: 8 wrapper: - "0.70.0/bio/kallisto/quant" + "v1.15.1/bio/kallisto/quant" rule kallisto_call_strains: diff --git a/workflow/rules/utils.smk b/workflow/rules/utils.smk index e9efda07f..0b8749070 100644 --- a/workflow/rules/utils.smk +++ b/workflow/rules/utils.smk @@ -14,7 +14,7 @@ rule tabix_index: log: "logs/tabix-{fmt}/{prefix}.log", wrapper: - "0.70.0/bio/tabix" + "v1.15.1/bio/tabix/index" rule bam_index: @@ -25,7 +25,7 @@ rule bam_index: log: "logs/bam-index/{prefix}.log", wrapper: - "0.70.0/bio/samtools/index" + "v1.15.1/bio/samtools/index" rule bcf_index: @@ -62,7 +62,7 @@ rule faidx: log: "logs/faidx/{prefix}.log", wrapper: - "0.70.0/bio/samtools/faidx" + "v1.15.1/bio/samtools/faidx" rule gzip: diff --git a/workflow/rules/variant_annotation.smk b/workflow/rules/variant_annotation.smk index 687eb73ad..2d58cec4f 100644 --- a/workflow/rules/variant_annotation.smk +++ b/workflow/rules/variant_annotation.smk @@ -12,7 +12,7 @@ rule get_vep_plugins: log: "logs/vep-plugins.log", wrapper: - "0.69.0/bio/vep/plugins" + "v1.15.1/bio/vep/plugins" rule annotate_variants: @@ -36,4 +36,4 @@ rule annotate_variants: log: "logs/{date}/vep/{annotation}/{sample}.log", wrapper: - "0.72.0/bio/vep/annotate" + "v1.15.1/bio/vep/annotate" diff --git a/workflow/rules/variant_calling.smk b/workflow/rules/variant_calling.smk index 8f757352c..ce9f060ec 100644 --- a/workflow/rules/variant_calling.smk +++ b/workflow/rules/variant_calling.smk @@ -10,9 +10,9 @@ rule freebayes: ref_idx=get_reference(".fai"), # you can have a list of samples here samples="results/{date}/recal/ref~{reference}/{sample}.bam", - index="results/{date}/recal/ref~{reference}/{sample}.bam.bai", + indexes="results/{date}/recal/ref~{reference}/{sample}.bam.bai", output: - temp("results/{date}/candidate-calls/ref~{reference}/{sample}.small.bcf"), + "results/{date}/candidate-calls/ref~{reference}/{sample}.small.bcf", params: # genotyping is performed by varlociraptor, hence we deactivate it in freebayes by # always setting --pooled-continuous @@ -22,7 +22,7 @@ rule freebayes: log: "logs/{date}/freebayes/ref~{reference}/{sample}.log", wrapper: - "0.80.1/bio/freebayes" + "v1.15.1/bio/freebayes" # TODO check delly single end mode @@ -33,7 +33,7 @@ rule delly: sample="results/{date}/recal/ref~{reference}/{sample}.bam", sample_idx="results/{date}/recal/ref~{reference}/{sample}.bam.bai", output: - temp("results/{date}/candidate-calls/ref~{reference}/{sample}.structural.bcf"), + "results/{date}/candidate-calls/ref~{reference}/{sample}.structural.bcf", log: "logs/{date}/delly/ref~{reference}/{sample}.log", conda: @@ -100,7 +100,7 @@ rule vcf_2_bcf: conda: "../envs/bcftools.yaml" shell: - "bcftools view -Oz -o {output} {input} 2> {log}" + "bcftools view -Oz -o {output} {input} 2> {log}" # TODO -Oz generates a .vcf.gz!! rule render_scenario: @@ -184,6 +184,6 @@ rule merge_varranges: log: "logs/{date}/merge-calls/ref~{reference}/{sample}.log", params: - "-a -Ob", + extra="-a", wrapper: - "0.69.0/bio/bcftools/concat" + "v1.15.1/bio/bcftools/concat" diff --git a/workflow/rules/variant_filtration.smk b/workflow/rules/variant_filtration.smk index 0c81778c3..ab81d6d2b 100644 --- a/workflow/rules/variant_filtration.smk +++ b/workflow/rules/variant_filtration.smk @@ -6,9 +6,9 @@ rule vembrane_filter: input: - "results/{date}/annotated-calls/ref~main/annot~{annotation}/{sample}.bcf", + vcf="results/{date}/annotated-calls/ref~main/annot~{annotation}/{sample}.bcf", output: - temp( + vcf=temp( "results/{date}/filtered-calls/ref~main/annot~{annotation}/{sample}.{filter}.bcf" ), params: @@ -17,7 +17,7 @@ rule vembrane_filter: log: "logs/{date}/vembrane/{sample}.{filter}.{annotation}.log", wrapper: - "0.71.1/bio/vembrane/filter" + "v1.15.1/bio/vembrane/filter" rule control_fdr: @@ -48,6 +48,6 @@ rule merge_calls: log: "logs/{date}/merge-calls/ref~{reference}/{sample}.{clonality}.{filter}.{annotation}.log", params: - "-a -Ob", + extra="-a", wrapper: - "0.69.0/bio/bcftools/concat" + "v1.15.1/bio/bcftools/concat"