Merge pull request #1400 from nschcolnicov/dev

ASSESS_SIGNIFICANCE fails with Rscript error fix

CHANGELOG.md

@@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
 - [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
 - [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
 
 ### Removed

README.md

@@ -157,6 +157,7 @@ We thank the following people for their extensive assistance in the development
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
+- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)

conf/modules/controlfreec.config

@@ -50,8 +50,7 @@ process {
         ]
     }
 
-    withName: 'MAKEGRAPH' {
-        ext.args   = { "${params.cf_ploidy}" }
+    withName: 'MAKEGRAPH2' {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },

modules.json

@@ -107,11 +107,10 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "controlfreec/makegraph": {
+                    "controlfreec/makegraph2": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
+                        "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",
+                        "installed_by": ["modules"]
                     },
                     "deepvariant": {
                         "branch": "master",

subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf

@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC              as FREEC_SOMATIC       } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED          as FREEC2BED           } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS       as FREEC2CIRCOS        } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH          as MAKEGRAPH           } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2         as MAKEGRAPH2           } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     take:
@@ -27,16 +27,39 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
 
     FREEC_SOMATIC(controlfreec_input, fasta, fasta_fai, [], dbsnp, dbsnp_tbi, chr_files, mappability, intervals_bed, [])
 
-    ASSESS_SIGNIFICANCE(FREEC_SOMATIC.out.CNV.join(FREEC_SOMATIC.out.ratio, failOnDuplicate: true, failOnMismatch: true))
+    //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file
+    //Creates empty channel if file is missing
+    cnv_files = FREEC_SOMATIC.out.CNV
+    .map{ meta, cnv ->
+        def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
+        if (!tumor_file){
+            error("CNVs tumor file not found for sample $meta.id")
+        }
+        [meta,tumor_file]
+    }
+
+    ratio_files = FREEC_SOMATIC.out.ratio
+    .map{ meta, ratio ->
+        def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
+        if (!tumor_file){
+            error("Ratio tumor file not found for sample $meta.id")
+        }
+        [meta,tumor_file]
+    }
+
+    //Join the pairs
+    assess_significance_input = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
+
+    ASSESS_SIGNIFICANCE(assess_significance_input)
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
-    MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_SOMATIC.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions

subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf

@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2 as MAKEGRAPH2                  } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     take:
@@ -30,13 +30,13 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     ASSESS_SIGNIFICANCE(FREEC_TUMORONLY.out.CNV.join(FREEC_TUMORONLY.out.ratio, failOnDuplicate: true, failOnMismatch: true))
     FREEC2BED(FREEC_TUMORONLY.out.ratio)
     FREEC2CIRCOS(FREEC_TUMORONLY.out.ratio)
-    MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions

tests/config/pytesttags.yml

@@ -248,7 +248,7 @@ controlfreec:
   - modules/nf-core/controlfreec/freec/**
   - modules/nf-core/controlfreec/freec2bed/**
   - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph2/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_mpileup/**
   - subworkflows/local/bam_variant_calling_somatic_all/**