Merge branch 'dev' into feature/enhancements_v2

mskcc-omics-workflows · Nov 20, 2024 · 7e39826 · 7e39826
2 parents f438ae0 + 64c65b2
commit 7e39826
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Showing 4 changed files with 29 additions and 7 deletions.
diff --git a/conf/juno.config b/conf/juno.config
@@ -7,10 +7,11 @@
 */
 
 executor {
-name = "lsf"
+    name = "lsf"
 }
 
 process {
-clusterOptions = ""
-scratch=false
+    clusterOptions = ""
+    scratch=false
 }
+
diff --git a/modules/local/bcftools/reheader/main.nf b/modules/local/bcftools/reheader/main.nf
@@ -8,7 +8,8 @@ process BCFTOOLS_REHEADER {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(samples)
+    tuple val(meta), path(vcf)
+    //, path(samples)
 
     output:
     tuple val(meta), path("*.vcf"), emit: sample_reordered_vcf
@@ -20,8 +21,10 @@ process BCFTOOLS_REHEADER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
-    bcftools reheader -s ${samples} -o ${vcf.BaseName}_reordered.vcf ${vcf}
+    echo -e "${meta.case_id}\n${meta.control_id}" > sampleorder.txt
+    bcftools reheader -s sampleorder.txt -o ${vcf.BaseName}_reordered.vcf ${vcf}
 
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/nextflow.config b/nextflow.config
@@ -183,6 +183,21 @@ singularity.registry = 'quay.io'
 // Nextflow plugins
 plugins {
     id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-prov'
+}
+
+prov {
+    enabled = true
+    formats {
+    bco {
+        file = "${params.outdir}/bco.json"
+        overwrite = true
+    }
+    legacy {
+        file = "${params.outdir}/manifest.json"
+        overwrite = true
+    }
+    }
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container

diff --git a/workflows/nucleovar.nf b/workflows/nucleovar.nf
@@ -90,7 +90,6 @@ workflow NUCLEOVAR {
 
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     PREPARE_INPUTS( case_bams,sample_id_names,Channel.from(params.target_bed) )
-
     target_bed_file = PREPARE_INPUTS.out.target_bed_file
 
     // processing subworkflows for each variant caller
@@ -161,6 +160,11 @@ workflow NUCLEOVAR {
 
     // // // // // // mpath loading script module
     TAG_BY_VARIANT_ANNOTATION( access_filtered_maf,canonical_tx_ref )
+    annotated_exonic_maf_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_exonic
+    annotated_silent_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_silent
+    annotated_nonpanel_exonic_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_nonpanel_exonic
+    annotated_nonpanel_silent_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_nonpanel_silent
+    annotated_dropped_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_dropped
 
     annotated_exonic_maf_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_exonic
     annotated_silent_file = TAG_BY_VARIANT_ANNOTATION.out.annotated_silent
@@ -187,7 +191,6 @@ workflow NUCLEOVAR {
     annotated_dropped_file
 
 
-
 }
 
 /*