fix: gatk4spark tests

nf-core · Jun 8, 2021 · 0dd07ea · 0dd07ea
1 parent b092ea3
commit 0dd07ea
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/modules/nf-core/software/gatk4/markduplicatesspark/main.nf b/modules/nf-core/software/gatk4/markduplicatesspark/main.nf
@@ -6,9 +6,10 @@ options        = initOptions(params.options)
 
 process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
-    label 'process_medium'
-    publishDir params.outdir, mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::gatk4-spark=4.2.0.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

diff --git a/subworkflows/local/build_indices.nf b/subworkflows/local/build_indices.nf
@@ -36,6 +36,7 @@ workflow BUILD_INDICES {
     take:
         dbsnp             // channel: [optional]  dbsnp
         fasta             // channel: [mandatory] fasta
+        fasta_fai         // channel: [optional]  fasta_fai
         germline_resource // channel: [optional]  germline_resource
         known_indels      // channel: [optional]  known_indels
         pon               // channel: [optional]  pon
@@ -55,6 +56,7 @@ workflow BUILD_INDICES {
         (result_dict, version_dict) = GATK4_DICT(fasta)
 
     result_fai = Channel.empty()
+    if (fasta_fai) result_fai = fasta_fai
     version_fai = Channel.empty()
     if (!(params.fasta_fai) && !('annotate' in params.step.toLowerCase()))
         (result_fai, version_fai) = SAMTOOLS_FAIDX(fasta)

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -21,6 +21,7 @@ checkPathParamList = [
     params.chr_length,
     params.dbsnp,
     params.fasta,
+    params.fasta_fai,
     params.germline_resource,
     params.input,
     params.known_indels,
@@ -44,7 +45,6 @@ else {
         case 'mapping': break
         case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
         case 'recalibrate':           csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break
-        case 'recalibrate':           csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break
         case 'variant_calling':       csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break
         // case 'controlfreec':          csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
         case 'annotate': break
@@ -94,6 +94,7 @@ chr_dir           = params.chr_dir           ? file(params.chr_dir)           :
 chr_length        = params.chr_length        ? file(params.chr_length)        : ch_dummy_file
 dbsnp             = params.dbsnp             ? file(params.dbsnp)             : ch_dummy_file
 fasta             = params.fasta             ? file(params.fasta)             : ch_dummy_file
+fasta_fai         = params.fasta_fai         ? file(params.fasta_fai)         : ch_dummy_file
 germline_resource = params.germline_resource ? file(params.germline_resource) : ch_dummy_file
 known_indels      = params.known_indels      ? file(params.known_indels)      : ch_dummy_file
 loci              = params.ac_loci           ? file(params.ac_loci)           : ch_dummy_file
@@ -206,6 +207,7 @@ workflow SAREK {
     BUILD_INDICES(
         dbsnp,
         fasta,
+        fasta_fai,
         germline_resource,
         known_indels,
         pon,