fix linting + reimplement only_call and only_merge

nf-cmgg · Nov 5, 2024 · 6eaf981 · 6eaf981
1 parent 76a86a2
commit 6eaf981
Show file tree

Hide file tree

Showing 5 changed files with 32 additions and 10 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -367,7 +367,7 @@ process {
     withName: "^.*VCF_FILTER_BCFTOOLS:FILTER_1\$" {
         ext.prefix = { "${meta.id}.filtered1" }
         ext.args = {
-            meta.caller == "vardict" ? 
+            meta.caller == "vardict" ?
                 "-i 'QUAL >= 0${params.only_pass ? " && FILTER=\"PASS\"" : ""}' --output-type z":
             meta.caller == "haplotypecaller" ?
                 "--output-type z --soft-filter 'GATKCutoffSNP' -e 'TYPE=\"snp\" && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0 || MQ < 30.0)' -m '+'":
@@ -378,7 +378,7 @@ process {
     }
 
     withName: "^.*VCF_FILTER_BCFTOOLS:FILTER_2\$" {
-        ext.args = { 
+        ext.args = {
             meta.caller == "vardict" ?
                 "--soft-filter 'LowFreqBias' --mode '+' -e  'FORMAT/AF[0:*] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z" :
             meta.caller == "haplotypecaller" ?

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -104,6 +104,24 @@
                     "format": "path",
                     "fa_icon": "fas fa-folder"
                 },
+                "elfasta": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.elfasta$",
+                    "description": "Path to the ELFASTA genome file. This is used when `elprep` is part of the callers and will be automatically generated when missing.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "elsites": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.elsites$",
+                    "description": "Path to the elsites file. This is used when `elprep` is part of the callers.",
+                    "fa_icon": "far fa-file-code"
+                },
                 "genomes_base": {
                     "type": "string",
                     "default": "/references/",

diff --git a/subworkflows/local/bam_call_elprep/main.nf b/subworkflows/local/bam_call_elprep/main.nf
@@ -35,7 +35,7 @@ workflow BAM_CALL_ELPREP {
         false
     )
     ch_versions = ch_versions.mix(ELPREP_FILTER.out.versions.first())
-    
+
     VCF_CONCAT_BCFTOOLS(
         ELPREP_FILTER.out.gvcf,
         true

diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test
@@ -46,7 +46,7 @@ nextflow_workflow {
                     },
                     workflow.out.ready_bams.collect {
                         [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
-                    },                    
+                    },
                     workflow.out.ready_beds,
                     workflow.out.reports
                 ).match("default - WGS") }
@@ -93,7 +93,7 @@ nextflow_workflow {
                     },
                     workflow.out.ready_bams.collect {
                         [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
-                    },                    
+                    },
                     workflow.out.ready_beds,
                     workflow.out.reports
                 ).match("default - WES common ROI") }
@@ -140,7 +140,7 @@ nextflow_workflow {
                     },
                     workflow.out.ready_bams.collect {
                         [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
-                    },                    
+                    },
                     workflow.out.ready_beds,
                     workflow.out.reports
                 ).match("default - WES") }

diff --git a/workflows/germline.nf b/workflows/germline.nf
@@ -384,7 +384,7 @@ workflow GERMLINE {
     //
     // Run sample preparation
     //
-    
+
     def create_bam_files = callers.intersect(GlobalVariables.bamCallers).size() > 0 // Only create BAM files when needed
     CRAM_PREPARE_SAMTOOLS_BEDTOOLS(
         ch_input.cram.filter { meta, _cram, _crai ->
@@ -491,10 +491,11 @@ workflow GERMLINE {
         ch_calls = ch_calls.mix(BAM_CALL_VARDICTJAVA.out.vcfs)
     }
 
-    // TODO reimplement --only_call and --only_merge
+    // Stop pipeline execution when only calls should happen
+    def ch_gvcfs_final = ch_gvcfs_ready.filter { !only_call }
 
     GVCF_JOINT_GENOTYPE_GATK4(
-        ch_gvcfs_ready,
+        ch_gvcfs_final,
         ch_fasta_ready,
         ch_fai_ready,
         ch_dict_ready,
@@ -506,7 +507,10 @@ workflow GERMLINE {
     ch_versions = ch_versions.mix(GVCF_JOINT_GENOTYPE_GATK4.out.versions)
     ch_calls = ch_calls.mix(GVCF_JOINT_GENOTYPE_GATK4.out.vcfs)
 
-    def ch_called_variants = ch_calls
+    // Stop pipeline execution when only the merge should happen
+    def ch_calls_final = ch_calls.filter { !only_merge }
+
+    def ch_called_variants = ch_calls_final
         .map { meta, vcf, tbi ->
             def new_meta = meta - meta.subMap(["type", "vardict_min_af"])
             [ new_meta, vcf, tbi ]