Fixing Lint

CHANGELOG.md

@@ -42,7 +42,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#20](https://github.com/nf-core/sarek/pull/20) - Add `markdownlint` config file
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add tests for latest Nextflow version as well
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add `genomes.config` for genomes without AWS iGenomes
-- [#24](https://github.com/nf-core/sarek/pull/24) - Added GATK4 Mutect2 calling and filtering 
+- [#24](https://github.com/nf-core/sarek/pull/24) - Added GATK4 Mutect2 calling and filtering
 - [#XXX](https://github.com/nf-core/sarek/pull/XXX) - Use Github actions for CI
 - [#31](https://github.com/nf-core/sarek/pull/31) - Add nf-core lint
 - [#31](https://github.com/nf-core/sarek/pull/31) - Add extra CI to GitHub Actions nf-core extra CI
@@ -75,7 +75,8 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#21](https://github.com/nf-core/sarek/pull/21) - Moved smallGRCh37 path to `genomes.config`
 - [#24](https://github.com/nf-core/sarek/pull/24) - iGenomes config now contains germline resource for GATK4 Mutect2
 - [#31](https://github.com/nf-core/sarek/pull/31) - Move extra CI to GitHub Actions nf-core extra CI
-- [#32](https://github.com/nf-core/sarek/pull/32) - Install `ASCAT` with `conda` in the `environment.yml` file
+- [#32](https://github.com/nf-core/sarek/pull/32), [#33](https://github.com/nf-core/sarek/pull/33) - Install `ASCAT` with `conda` in the `environment.yml` file
+- [#33](https://github.com/nf-core/sarek/pull/33) - use workflow.manifest.version to specify workflow version in path to R scripts for control-FREEC and VEP processes
 
 ### `Removed`
 
@@ -101,6 +102,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#22](https://github.com/nf-core/sarek/pull/22) - Fix --singleCPUMem issue
 - [#31](https://github.com/nf-core/sarek/pull/31) - Fix badges according to nf-core lint
 - [#31](https://github.com/nf-core/sarek/pull/31) - Fix rcolorbrewer version according to nf-core lint
+- [#33](https://github.com/nf-core/sarek/pull/33) - Fix MD Linting
 
 ## [2.3.FIX1] - 2019-03-04
 

bin/scrape_software_versions.py

@@ -5,7 +5,7 @@
 
 regexes = {
     'AlleleCount': ['v_allelecount.txt', r"(\S+)"],
-    'ASCAT': ['v_ascat.txt', r"(\d\.\d+)"],
+    'ASCAT': ['v_ascat.txt', r"Version:       (\S+)"],
     'bcftools': ['v_bcftools.txt', r"bcftools (\S+)"],
     'BWA': ['v_bwa.txt', r"Version: (\S+)"],
     'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],

docs/output.md

@@ -144,9 +144,8 @@ For all samples:
 
 [GATK Mutect2](https://github.com/broadinstitute/gatk) calls somatic SNVs and indels via local assembly of haplotypes.
 
-For further reading and documentation see the [Mutect2 manual](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php). 
-It is recommended to have panel of normals [PON](https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2) for this version of Mutect2 using at 
-least 40 normal samples, and you can add your PON file to get filtered somatic calls. 
+For further reading and documentation see the [Mutect2 manual](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php).
+It is recommended to have panel of normals [PON](https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2) for this version of Mutect2 using at least 40 normal samples, and you can add your PON file to get filtered somatic calls.
 
 For a Tumor/Normal pair only:
 **Output directory: `results/VariantCalling/[TUMOR_vs_NORMAL]/Mutect2`**

docs/usage.md

@@ -314,17 +314,24 @@ If you prefer, you can specify the full path to your reference genome when you r
 --genomeIndex '[path to the genome Index]'
 ```
 
-
 ### `--germlineResource`
+
+The [germline resource VCF file](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php#--germline-resource) (bgzipped and tabixed) needed by GATK4 Mutect2 is a collection of calls that are likely present in the sample, with allele frequencies.
+The AF info field must be present.
+You can find a smaller, stripped gnomAD VCF file (most of the annotation is removed and only calls signed by PASS are stored) in the iGenomes Annotation/GermlineResource folder.
+To add your own germline resource supply
+
+```bash
+--germlineResource '[path to my resource.vcf.gz]'
+```
+
 ### `--germlineResourceIndex`
 
-The [germline resource VCF file](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php#--germline-resource) (bgzipped and tabixed) needed 
-by GATK4 Mutect2 is a collection of calls that are likely present in the sample, with allele frequencies. The AF info field must be present. 
-You can find a smaller, stripped gnomAD VCF file (most of the annotation is removed and only calls signed by PASS are stored) in the iGenomes Annotation/GermlineResource folder. To add your own
-germline resource supply
+Tabix index of the germline resource specified at [`--germlineResource`](#--germlineResource).
+To add your own germline resource supply
 
 ```bash
---germlineResource '[path to my resource.vcf.gz]' --germlineResourceIndex '[path to my resource.vcf.gz.idx]'
+--germlineResourceIndex '[path to my resource.vcf.gz.idx]'
 ```
 
 ### `--intervals`
@@ -353,19 +360,18 @@ If you prefer, you can specify the full path to your reference genome when you r
 
 ### `--pon`
 
-When a panel of normals [PON](https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest) is defined, you will get filtered 
-somatic calls as a result. Without PON, there will be no calls with PASS in the INFO field, only an _unfiltered_ VCF is written. It is recommended to make your own panel-of-normals, 
-as it depends on sequencer and library preparation. For tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it _should not be used_ as a
-real panel-of-normals file. Provide your PON by:
-
+When a panel of normals [PON](https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest) is defined, you will get filtered somatic calls as a result.
+Without PON, there will be no calls with PASS in the INFO field, only an _unfiltered_ VCF is written.
+It is recommended to make your own panel-of-normals, as it depends on sequencer and library preparation.
+For tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it _should not be used_ as a real panel-of-normals file.
+Provide your PON by:
 
 ```bash
 --pon '[path to the PON VCF]'
 ```
 
 If the PON file is bgzipped, there have to be a tabixed index file at the same directory.
 
-
 ### `--snpeffDb`
 
 If you prefer, you can specify the DB version when you run the pipeline:

main.nf

@@ -263,7 +263,6 @@ process GetSoftwareVersions {
     alleleCounter --version &> v_allelecount.txt  || true
     bcftools version > v_bcftools.txt 2>&1 || true
     bwa &> v_bwa.txt 2>&1 || true
-    cat ${baseDir}/scripts/ascat.R | grep "ASCAT version" &> v_ascat.txt  || true
     configManta.py --version > v_manta.txt 2>&1 || true
     configureStrelkaGermlineWorkflow.py --version > v_strelka.txt 2>&1 || true
     echo "${workflow.manifest.version}" &> v_pipeline.txt 2>&1 || true
@@ -275,6 +274,7 @@ process GetSoftwareVersions {
     multiqc --version &> v_multiqc.txt 2>&1 || true
     qualimap --version &> v_qualimap.txt 2>&1 || true
     R --version &> v_r.txt  || true
+    R -e "library(ASCAT); help(package='ASCAT')" &> v_ascat.txt
     samtools --version &> v_samtools.txt 2>&1 || true
     tiddit &> v_tiddit.txt 2>&1 || true
     vcftools --version &> v_vcftools.txt 2>&1 || true
@@ -1803,12 +1803,12 @@ process ControlFreecViz {
     when: 'controlfreec' in tools
 
     """
-    cat /opt/conda/envs/sarek-2.5dev/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}
-    cat /opt/conda/envs/sarek-2.5dev/bin/assess_significance.R | R --slave --args ${cnvNormal} ${ratioNormal}
-    cat /opt/conda/envs/sarek-2.5dev/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
-    cat /opt/conda/envs/sarek-2.5dev/bin/makeGraph.R | R --slave --args 2 ${ratioNormal} ${bafNormal}
-    perl /opt/conda/envs/sarek-2.5dev/bin/freec2bed.pl -f ${ratioTumor} > ${idSampleTumor}.bed
-    perl /opt/conda/envs/sarek-2.5dev/bin/freec2bed.pl -f ${ratioNormal} > ${idSampleNormal}.bed
+    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}
+    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvNormal} ${ratioNormal}
+    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
+    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioNormal} ${bafNormal}
+    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioTumor} > ${idSampleTumor}.bed
+    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioNormal} > ${idSampleNormal}.bed
     """
 }
 
@@ -2069,7 +2069,7 @@ process VEP {
     genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
     dir_cache = (params.vep_cache && params.annotation_cache) ? " \${PWD}/${dataDir}" : "/.vep"
     cadd = (params.cadd_cache && params.cadd_WG_SNVs && params.cadd_InDels) ? "--plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz" : ""
-    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-2.5dev/bin/genesplicer,/opt/conda/envs/sarek-2.5dev/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
+    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
     """
     mkdir ${reducedVCF}
 
@@ -2132,7 +2132,7 @@ process VEPmerge {
     genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
     dir_cache = (params.vep_cache && params.annotation_cache) ? " \${PWD}/${dataDir}" : "/.vep"
     cadd = (params.cadd_cache && params.cadd_WG_SNVs && params.cadd_InDels) ? "--plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz" : ""
-    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-2.5dev/bin/genesplicer,/opt/conda/envs/sarek-2.5dev/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
+    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
     """
     mkdir ${reducedVCF}