nf-core modules update -a

CHANGELOG.md

@@ -53,7 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#416](https://github.com/nf-core/sarek/pull/416) - Sync `TEMPLATE` with `tools` `2.1`
 - [#417](https://github.com/nf-core/sarek/pull/417) - Merge `dsl2` and `dev` branches
 - [#419](https://github.com/nf-core/sarek/pull/419) - Improve preprocessing
-- [#420](https://github.com/nf-core/sarek/pull/420), [#455](https://github.com/nf-core/sarek/pull/455), [#459](https://github.com/nf-core/sarek/pull/459) - `nf-core modules update --all`
+- [#420](https://github.com/nf-core/sarek/pull/420), [#455](https://github.com/nf-core/sarek/pull/455), [#459](https://github.com/nf-core/sarek/pull/459), [#633](https://github.com/nf-core/sarek/pull/633) - `nf-core modules update --all`
 - [#427](https://github.com/nf-core/sarek/pull/427) - Update `DeepVariant`
 - [#462](https://github.com/nf-core/sarek/pull/462) - Update modules and `modules.config`
 - [#465](https://github.com/nf-core/sarek/pull/465) - Improve `test_data.config`
@@ -82,12 +82,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
 - [#606](https://github.com/nf-core/sarek/pull/606) - Updated `ASCAT` to version `3.0` as module
 - [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta
+- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module
+- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
 - [#620](https://github.com/nf-core/sarek/pull/620) - `gender` is now `sex` in the samplesheet
 - [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file
 - [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105`
 - [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
-- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
-- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
+- [#633](https://github.com/nf-core/sarek/pull/633) - Update `BCFTOOLS` version to `1.15.1`
 - [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
 - [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
 - [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`

conf/modules.config

@@ -295,19 +295,24 @@ process {
 // MARKDUPLICATES
 
     withName: 'SAMTOOLS_CRAMTOBAM.*'{
-        ext.args = "-b"
+        ext.args         = "-b"
+    }
+
+
+    withName: 'SAMTOOLS_STATS_CRAM'{
+        ext.prefix       = { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${meta.id}.sorted.cram" : "${meta.id}.md.cram" }
     }
 
     withName: 'SAMTOOLS_BAMTOCRAM.*' {
         // BAM provided for step Markduplicates either run through MD or Convert -> then saved as md.cram
         // BAM files provided for step prepare_recal are converted and run through BQSR -> then saved as md.cram
         // BAM files provided for step recal are converted and run through BQSR II -> then saved as md.cram
-        ext.args = "-C"
-        ext.prefix       = { "${meta.id}.md" }
+        ext.args         = "-C"
+        ext.prefix       = { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${meta.id}.sorted" : "${meta.id}.md" }
         publishDir       = [
             enabled: !params.save_output_as_bam,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
+            path: { (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) ? "${params.outdir}/preprocessing/${meta.id}/mapped" : "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
             pattern: "*{cram,crai}"
         ]
     }
@@ -468,6 +473,12 @@ process {
         ]
     }
 
+    if (params.step == 'mapping' || params.step == 'markduplicates') {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_QC:SAMTOOLS_STATS' {
+            ext.prefix       = { "${meta.id}.cram" }
+        }
+    }
+
     withName: 'SAMTOOLS_STATS' {
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
         publishDir       = [
@@ -479,7 +490,7 @@ process {
 
     withName: 'MOSDEPTH' {
         ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
-        ext.prefix       = { "${meta.id}.md" }
+        ext.prefix       = { params.skip_tools && params.skip_tools.split(',').contains('markduplicates') ? "${meta.id}.sorted" : "${meta.id}.md" }
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
         publishDir = [
             mode: params.publish_dir_mode,
@@ -494,6 +505,7 @@ process {
         }
 
         withName: 'NFCORE_SAREK:SAREK:CRAM_QC:SAMTOOLS_STATS' {
+            ext.prefix       = { "${meta.id}.recal.cram" }
             ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
             publishDir       = [
                 mode: params.publish_dir_mode,
@@ -700,7 +712,7 @@ process{
         ]
     }
     withName : 'TABIX_BGZIP_TIDDIT_SV' {
-        ext.prefix       = { "${meta.id}.tiddit.vcf" }
+        ext.prefix       = { "${meta.id}.tiddit" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
@@ -1091,11 +1103,11 @@ process{
     if (params.tools && params.tools.split(',').contains('tiddit')) {
     //TIDDIT
         withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
-            ext.prefix       = {"${meta.id}.tiddit.normal.vcf"}
+            ext.prefix       = {"${meta.id}.tiddit.normal"}
         }
 
         withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
-            ext.prefix       = {"${meta.id}.tiddit.tumor.vcf"}
+            ext.prefix       = {"${meta.id}.tiddit.tumor"}
         }
 
         //SVDB
@@ -1202,7 +1214,7 @@ process{
     // ALL ANNOTATION TOOLS
     if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: "NFCORE_SAREK:SAREK:ANNOTATE:.*:TABIX_BGZIPTABIX" {
-            ext.prefix       = { "${input}" }
+            ext.prefix       = { input.baseName.minus(".vcf") }
             publishDir       = [
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },

conf/test.config

@@ -220,9 +220,11 @@ process {
         }
     }
 
-    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
-        //sample name from when the test data was generated
-        ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
+    if (params.tools && params.tools.split(',').contains('mutect2')) {
+        withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
+            //sample name from when the test data was generated
+            ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
+        }
     }
 
     withName: 'FILTERVARIANTTRANCHES'{

modules.json

@@ -7,10 +7,10 @@
                 "git_sha": "98ffb090029d17a9fb8de75dadcfe6bc8b6377ec"
             },
             "bcftools/sort": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
             },
             "bcftools/stats": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
             },
             "bwa/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -55,7 +55,7 @@
                 "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
             },
             "deepvariant": {
                 "git_sha": "fd5f6f5f4ffef4ab5a4e809bd3211bbc71c38d30"
@@ -121,7 +121,7 @@
                 "git_sha": "175ea9b7f95a0e2fd3679f7a052c6dcb60b61a6e"
             },
             "gatk4/gatherbqsrreports": {
-                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
+                "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
             },
             "gatk4/gatherpileupsummaries": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
@@ -136,7 +136,7 @@
                 "git_sha": "1ac223ad436c1410e9c16a5966274b7ca1f8d855"
             },
             "gatk4/haplotypecaller": {
-                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
+                "git_sha": "e53d091a6de1ae9fd681351c085d8abe076ba1ec"
             },
             "gatk4/intervallisttobed": {
                 "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
@@ -208,7 +208,7 @@
                 "git_sha": "24e05f6097a5dde57dd80d33295ed120f1b81aef"
             },
             "samtools/stats": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"
             },
             "samtools/view": {
                 "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
@@ -226,7 +226,7 @@
                 "git_sha": "313d76e00525c8e975dabce0c34973fd53c3f4dd"
             },
             "tabix/bgziptabix": {
-                "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
+                "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b"
             },
             "tabix/tabix": {
                 "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484"

subworkflows/local/germline_variant_calling.nf

@@ -42,7 +42,6 @@ workflow GERMLINE_VARIANT_CALLING {
     strelka_vcf         = Channel.empty()
     tiddit_vcf          = Channel.empty()
 
-    println tools
     // Remap channel with intervals
     cram_recalibrated_intervals = cram_recalibrated.combine(intervals)
         .map{ meta, cram, crai, intervals, num_intervals ->
@@ -117,7 +116,11 @@ workflow GERMLINE_VARIANT_CALLING {
 
     // HAPLOTYPECALLER
     if (tools.split(',').contains('haplotypecaller')){
-        RUN_HAPLOTYPECALLER(cram_recalibrated_intervals,
+        cram_recalibrated_intervals_haplotypecaller = cram_recalibrated_intervals
+            .map{ meta, cram, crai, intervals ->
+                [meta, cram, crai, intervals, []]
+            }
+        RUN_HAPLOTYPECALLER(cram_recalibrated_intervals_haplotypecaller,
                         fasta,
                         fasta_fai,
                         dict,