Merge pull request #204 from MaxUlysse/ControlFREEC

Control-FREEC improvements
nf-core · May 18, 2020 · fdbdaac · fdbdaac
2 parents 5db3d24 + edd53b1
commit fdbdaac
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,39 +6,42 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
+      SAREK_TAG: dev
     steps:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+          command: docker build -t nfcore/sareksnpeff:${SAREK_TAG}.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
       - run:
-          command: |
-            echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-            docker push nfcore/sareksnpeff:dev.${GENOME}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sareksnpeff:${SAREK_TAG}.${GENOME}
 
   snpeffgrch38:
     << : *buildsnpeff
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   vepgrch37: &buildvep
     docker:
@@ -47,42 +50,47 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
+      SAREK_TAG: dev
     steps:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sarekvep:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          command: docker build -t nfcore/sarekvep:${SAREK_TAG}.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
           no_output_timeout: 3h
       - run:
-          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:dev.${GENOME}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:${SAREK_TAG}.${GENOME}
 
   vepgrch38:
     << : *buildvep
     environment:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
 workflows:
   version: 2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#195](https://github.com/nf-core/sarek/pull/195) - Now creating TSV for duplicates marked BAMs in minimal setting
 - [#195](https://github.com/nf-core/sarek/pull/195), [#202](https://github.com/nf-core/sarek/pull/202) - Add `--save_bam_mapped` params to save mapped BAMs.
 - [#197](https://github.com/nf-core/sarek/pull/197) - Add step `prepare_recalibration` to allow restart from DuplicatesMarked BAMs
+- [#204](https://github.com/nf-core/sarek/pull/204) - Add step `Control-FREEC` to allow restart from pileup files
 
 ### Changed
 
@@ -56,11 +57,10 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
 - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
 - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`
-- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158), [#164](https://github.com/nf-core/sarek/pull/164), [#174](https://github.com/nf-core/sarek/pull/174), [#194](https://github.com/nf-core/sarek/pull/194) - Update docs
+- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158), [#164](https://github.com/nf-core/sarek/pull/164), [#174](https://github.com/nf-core/sarek/pull/174), [#194](https://github.com/nf-core/sarek/pull/194), [#198](https://github.com/nf-core/sarek/pull/198), [#204](https://github.com/nf-core/sarek/pull/204) - Update docs
 - [#164](https://github.com/nf-core/sarek/pull/164) - Update `gatk4-spark` from `4.1.4.1` to `4.1.6.0`
 - [#180](https://github.com/nf-core/sarek/pull/180), [#195](https://github.com/nf-core/sarek/pull/195) - Improve minimal setting
-- [#183](https://github.com/nf-core/sarek/pull/183) - Update `input.md` documentation
-- [#198](https://github.com/nf-core/sarek/pull/198) - Update docs
+- [#183](https://github.com/nf-core/sarek/pull/183), [#204](https://github.com/nf-core/sarek/pull/204) - Update `input.md` documentation
 
 ### Fixed
 

diff --git a/conf/genomes.config b/conf/genomes.config
@@ -25,6 +25,7 @@ params {
       intervals               = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
       known_indels            = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       known_indels_index      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
+      mappability             = "${params.genomes_base}/out100m2_hg19.gem"
       snpeff_db               = 'GRCh37.75'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
@@ -45,6 +46,7 @@ params {
       intervals               = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
       known_indels            = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       known_indels_index      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
+      mappability             = "${params.genomes_base}/out100m2_hg38.gem"
       snpeff_db               = 'GRCh38.86'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -25,6 +25,7 @@ params {
       intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
       known_indels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       known_indels_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
+      mappability             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
       snpeff_db               = 'GRCh37.75'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
@@ -45,6 +46,7 @@ params {
       intervals               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
       known_indels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       known_indels_index      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
+      mappability             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
       snpeff_db               = 'GRCh38.86'
       species                 = 'homo_sapiens'
       vep_cache_version       = '99'
@@ -61,6 +63,7 @@ params {
       intervals               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
       known_indels            = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
       known_indels_index      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
+      mappability             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
       snpeff_db               = 'GRCm38.86'
       species                 = 'mus_musculus'
       vep_cache_version       = '99'

diff --git a/docs/input.md b/docs/input.md
@@ -16,8 +16,9 @@ For all possible TSV files, described in the next sections, here is an explanati
 - `bam` is the path to the bam file
 - `bai` is the path to the bam index file
 - `recaltable` is the path to the recalibration table
+- `mpileup` is the path to the mpileup file
 
-It is recommended to add the absolute path of the files, but relative path should work also.
+It is recommended to add the absolute path of the files, but relative path should also work.
 Note, the delimiter is the tab (`\t`) character.
 
 All examples are given for a normal/tumor pair.
@@ -172,6 +173,25 @@ When starting Sarek from the mapping or recalibrate steps, a TSV file is generat
 
 Additionally, individual TSV files for each sample (`recalibrated_[SAMPLE].tsv`) can be found in the same directory.
 
+## Starting from the mpileup file with the Control-FREEC step
+
+To start from the Control-FREEC step (`--step Control-FREEC`), a TSV file for a normal/tumor pair needs to be given as input containing the paths to the mpileup files.
+The TSV needs to contain the following columns:
+
+- `subject sex status sample mpileup`
+
+The same way, if you have non recalibrated BAMs and their indexes, you should use a structure like:
+
+```text
+G15511    XX    0    C09DFN    pathToFiles/G15511.C09DFN.pileup
+G15511    XX    1    D0ENMT    pathToFiles/G15511.D0ENMT.pileup
+```
+
+When starting Sarek from the Control-FREEC step, a TSV file is generated automatically after the `mpileup` process.
+This TSV file is stored under `results/VariantCalling/TSV/control-freec_mpileup.tsv` and can be used to restart Sarek from the mpileup files. Setting the step `--step Control-FREEC` will automatically take this file as input.
+
+Additionally, individual TSV files for each sample (`control-freec_mpileup_[SAMPLE].tsv`) can be found in the same directory.
+
 ## VCF files for annotation
 
 Input files for Sarek can be specified using the path to a VCF directory given to the `--input` command only with the annotation step (`--step annotate`).