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nf-core · Sep 13, 2023 · 9c1f1c0 · 9c1f1c0
1 parent e4fe05b
commit 9c1f1c0
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Showing 8 changed files with 9 additions and 319 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,7 +10,7 @@
             "sample": {
                 "type": "string",
                 "exists": true,
-                "meta": ["id"],
+                "meta": ["id", "sample"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },

diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf
@@ -7,7 +7,7 @@ include { ALIGN_SENTIEON             } from './alignment/align_sentieon'
 include { SAMTOOLS_VIEW              } from '../../modules/nf-core/samtools/view/main'
 include { ALIGN_MT                   } from './alignment/align_MT'
 include { ALIGN_MT as ALIGN_MT_SHIFT } from './alignment/align_MT'
-include { CONVERT_MT_BAM_TO_FASTQ    } from './convert_mt_bam_to_fastq'
+include { CONVERT_MT_BAM_TO_FASTQ    } from './mitochondria/convert_mt_bam_to_fastq'
 
 workflow ALIGN {
     take:

diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf
@@ -36,12 +36,12 @@ workflow ANNOTATE_MT_SNVS {
 
         // Pick input for vep
         ch_mt_vcf
-            .combine(ANNOTATE_CADD.out.vcf.ifEmpty("null"))
-            .branch { it  ->
-                merged: it[2].equals("null")
+            .join(ANNOTATE_CADD.out.vcf, remainder: true) // If CADD is not run then the third element in this channel will be `null`
+            .branch { it  ->                              // If CADD is run, then "it" will be [[meta],selvar.vcf,cadd.vcf], else [[meta],selvar.vcf,null]
+                merged: it[2].equals(null)
                     return [it[0], it[1]]
-                cadd: !(it[2].equals("null"))
-                    return [it[2], it[3]]
+                cadd: !(it[2].equals(null))
+                    return [it[0], it[2]]
             }
             .set { ch_for_mix }
         ch_vep_in = ch_for_mix.merged.mix(ch_for_mix.cadd)

diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf
@@ -50,8 +50,6 @@ workflow CALL_STRUCTURAL_VARIANTS {
 
         CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta)
 
-//        CALL_SV_MT_SHIFT (ch_mtshift_bam_bai, ch_mtshift_fasta)
-
         //merge
         if (params.skip_cnv_calling) {
             tiddit_vcf

diff --git a/subworkflows/local/convert_mt_bam_to_fastq.nf b/subworkflows/local/convert_mt_bam_to_fastq.nf
diff --git a/subworkflows/local/mitochondria/align_and_call_MT.nf b/subworkflows/local/mitochondria/align_and_call_MT.nf
diff --git a/subworkflows/local/mitochondria/merge_annotate_MT.nf b/subworkflows/local/mitochondria/merge_annotate_MT.nf
diff --git a/subworkflows/local/variant_calling/postprocess_MT_calls.nf b/subworkflows/local/variant_calling/postprocess_MT_calls.nf
@@ -1,5 +1,5 @@
 //
-// Merge and annotate MT
+// Merge and normalize MT variants
 //
 
 include { GATK4_MERGEVCFS as GATK4_MERGEVCFS_LIFT_UNLIFT_MT     } from '../../../modules/nf-core/gatk4/mergevcfs/main'
@@ -25,7 +25,7 @@ workflow POSTPROCESS_MT_CALLS {
     main:
         ch_versions = Channel.empty()
 
-        // LIFTOVER VCF FROM REFERENCE MT TO SHIFTED MT
+        // LIFTOVER SHIFTED VCF TO REFERENCE MT POSITIONS
         PICARD_LIFTOVERVCF (
             ch_mtshift_vcf,
             ch_genome_dictionary,