change mitosalt input to mt fastq

CHANGELOG.md

@@ -65,6 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Update saltshaker modules to version 1.1.1 so they can run on empty mitosalt output [#856](https://github.com/nf-core/raredisease/pull/856)
 - Update metromap to reflect the addition of mitosalt + saltshaker and removal of eklipse [#892](https://github.com/nf-core/raredisease/pull/892)
 - Changed default glnexus config from `DeepVariant_unfiltered` to a custom config in `assets/` due to unfixed [bug](https://github.com/dnanexus-rnd/GLnexus/issues/286) [issue #960](https://github.com/nf-core/raredisease/issues/960) [PR #961](https://github.com/nf-core/raredisease/pull/961)
+- Change input file for mitosalt from genome-wide fastq to mitochondrial fastq [PR #967](https://github.com/nf-core/raredisease/pull/967)
 
 ### `Fixed`
 

conf/modules/call_sv_MT.config

@@ -22,6 +22,10 @@ process {
         ext.prefix = { "${meta.id}_mitochondria_deletions" }
     }
 
+    withName: '.*CALL_SV_MT:SEQTK_SAMPLE' {
+        ext.prefix = { "${meta.id}.sampled" }
+    }
+
     withName: '.*CALL_SV_MT:SALTSHAKER_CALL' {
         ext.args = '--blacklist'
     }

modules/local/prep_mitosalt/main.nf

@@ -68,12 +68,12 @@ process PREP_MITOSALT {
     echo "flank = ${flank}"                                       >> mitosalt_config.txt
     echo "split_distance_threshold = ${split_distance_threshold}" >> mitosalt_config.txt
     echo "dna = yes"                                              >> mitosalt_config.txt
-    echo "enriched = no"                                          >> mitosalt_config.txt
-    echo "nu_mt = yes"                                            >> mitosalt_config.txt
+    echo "enriched = yes"                                         >> mitosalt_config.txt
+    echo "nu_mt = no"                                             >> mitosalt_config.txt
     echo "rmtmp = no"                                             >> mitosalt_config.txt
     echo "o_mt = yes"                                             >> mitosalt_config.txt
     echo "i_del = yes"                                            >> mitosalt_config.txt
-    echo "cn_mt = yes"                                            >> mitosalt_config.txt
+    echo "cn_mt = no"                                             >> mitosalt_config.txt
     """
 
     stub:

subworkflows/local/align_mitochondria/main.nf

@@ -31,14 +31,15 @@ workflow ALIGN_MITOCHONDRIA {
             ch_genome_fai,
             ch_genome_fasta
         )
+        ch_mt_fastq = CONVERT_MT_BAM_TO_FASTQ.out.fastq
 
         ALIGN_MT (
             ch_mt_bwaindex,
             ch_mt_bwamem2index,
             ch_mt_dictionary,
             ch_mt_fai,
             ch_mt_fasta,
-            CONVERT_MT_BAM_TO_FASTQ.out.fastq,
+            ch_mt_fastq,
             CONVERT_MT_BAM_TO_FASTQ.out.ubam,
             val_mt_aligner
         )
@@ -49,7 +50,7 @@ workflow ALIGN_MITOCHONDRIA {
             ch_mtshift_dictionary,
             ch_mtshift_fai,
             ch_mtshift_fasta,
-            CONVERT_MT_BAM_TO_FASTQ.out.fastq,
+            ch_mt_fastq,
             CONVERT_MT_BAM_TO_FASTQ.out.ubam,
             val_mt_aligner
         )
@@ -61,6 +62,7 @@ workflow ALIGN_MITOCHONDRIA {
                                         .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling
 
     emit:
+        mt_fastq                  = ch_mt_fastq                  // channel: [ val(meta), [ path(fastq) ] ]
         mt_bam_bai                = ch_mt_bam_bai                // channel: [ val(meta), path(bam), path(bai) ]
         mt_bam_bai_gatksubwf      = ch_mt_bam_bai_gatksubwf      // channel: [ val(meta), path(bam), path(bai) ]
         mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ]

subworkflows/local/call_sv_MT/main.nf

@@ -25,7 +25,7 @@ workflow CALL_SV_MT {
         ch_mt_fai                             // channel: [mandatory] [ val(meta), path(mtfai) ]
         ch_mt_fasta                           // channel: [mandatory] [ val(meta), path(mtfasta) ]
         ch_mt_lastdb                          // channel: [mandatory] [ val(meta), path(lastindex) ]
-        ch_reads                              // channel: [mandatory] [ val(meta), [path(reads)] ]
+        ch_mt_fastq                           // channel: [mandatory] [ val(meta), [path(fastq)] ]
         ch_subdepth                           // channel: [mandatory] [ val(mitosalt_depth) ]
         ch_svcaller_priority                  // channel: [mandatory] [ val(["var caller tag 1", ...]) ]
         ch_mitosalt_config                    // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)]
@@ -45,27 +45,8 @@ workflow CALL_SV_MT {
         ch_saltshaker_plot  = channel.empty()
 
         if (!skip_mitosalt) {
-            ch_cat_fastq = ch_reads
-                .map { meta, reads ->
-                        def sample_group_key = meta.sample
-                        return [sample_group_key, meta, reads]
-                }
-                .groupTuple()
-                .map { sample_id, meta_list, reads_list ->
-                    def combined_meta = meta_list[0].clone()
-                    combined_meta.id = sample_id
-                    combined_meta.remove('lane')
-                    combined_meta.remove('read_group')
-
-                    def all_reads = reads_list.flatten()
-
-                    [combined_meta, all_reads]
-                }
-
-            CAT_FASTQ(ch_cat_fastq)
-
-            ch_reads_subdepth = CAT_FASTQ.out.reads.combine(ch_subdepth)
 
+            ch_reads_subdepth = ch_mt_fastq.combine(ch_subdepth)
             SEQTK_SAMPLE(ch_reads_subdepth)
 
             PREP_MITOSALT(