Merge branch 'CW-2369' into 'dev'

Resolve CW-2369

Closes CW-2369

See merge request epi2melabs/workflows/wf-transcriptomes!138

CHANGELOG.md

@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 ### Added
+- Published minimap2 and pychopper results to output directory.
 - Two extra pychopper parameters `--cdna_kit` and `--pychopper_backend`. `--pychopper_options` is still available to define any other options.
 
 ## [v0.4.2]

main.nf

@@ -142,21 +142,32 @@ process preprocess_reads {
     cpus 4
     memory "2 GB"
     input:
-        tuple val(meta), path(input_reads)
+        tuple val(meta), path('seqs.fastq.gz')
     output:
-         tuple val("${meta.alias}"), path("${meta.alias}_full_length_reads.fastq"), emit: full_len_reads
+        tuple val("${meta.alias}"),
-         path '*.tsv',  emit: report
+              path("${meta.alias}_pychopper_output/${meta.alias}_full_length_reads.fastq"),
+              emit: full_len_reads
+        tuple val("${meta.alias}"),
+              path("${meta.alias}_pychopper_output/"),
+              emit: pychopper_output
+        path "${meta.alias}_pychopper_output/${meta.alias}_pychopper.tsv",
+              emit: report
     script:
         def cdna_kit = params.cdna_kit.split("-")[-1]
 	    def extra_params = params.pychopper_opts ?: ''    
         """
-        pychopper -t ${params.threads} -k ${cdna_kit} -m ${params.pychopper_backend} ${extra_params} ${input_reads} ${meta.alias}_full_length_reads.fastq
+        pychopper -t ${params.threads} -k ${cdna_kit} -m ${params.pychopper_backend} ${extra_params} 'seqs.fastq.gz' ${meta.alias}_full_length_reads.fastq
         mv pychopper.tsv ${meta.alias}_pychopper.tsv
         workflow-glue generate_pychopper_stats --data ${meta.alias}_pychopper.tsv --output .
 
-        # Add sample id column
+        # Add sample id colum
         sed "1s/\$/\tsample_id/; 1 ! s/\$/\t${meta.alias}/" ${meta.alias}_pychopper.tsv > tmp
         mv tmp ${meta.alias}_pychopper.tsv
+
+
+        mkdir "${meta.alias}_pychopper_output/"
+        shopt -s extglob  # Allow extended pattern matching so we can exclude files from the mv
+        mv !("${meta.alias}_pychopper_output"|seqs.fastq.gz) "${meta.alias}_pychopper_output/"
         """
 }
 
@@ -541,7 +552,7 @@ workflow pipeline {
         }
 
      
-
+        results = Channel.empty()
         software_versions = getVersions()
         workflow_params = getParams()
         input_reads = reads.map{ meta, samples, stats -> [meta, samples]}
@@ -552,6 +563,8 @@ workflow pipeline {
             preprocess_reads(input_reads)
             full_len_reads = preprocess_reads.out.full_len_reads
             pychopper_report = preprocess_reads.out.report.collectFile(keepHeader: true)
+            pychopper_results_dir = preprocess_reads.out.pychopper_output.map{ it -> it[1]}
+            results = results.concat(pychopper_results_dir)
         }
         else{
             full_len_reads = input_reads.map{ meta, reads -> [meta.alias, reads]}
@@ -564,7 +577,7 @@ workflow pipeline {
         
             assembly_stats = assembly.stats.map{ it -> it[1]}.collect()
      
-            split_bam(assembly.bam)
+            split_bam(assembly.bam.map {sample_id, bam, bai -> [sample_id, bam]})
 
             assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann)
 
@@ -582,14 +595,14 @@ workflow pipeline {
 
             gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
             merge_gff = merge_gff_bundles.out.gff.map{ it -> it[1]}.collect()
-            results = Channel.empty()
+            results = results.concat(assembly.bam.map {sample_id, bam, bai -> [bam, bai]}.flatten())
-        }else
+        }
-        {
+        else{
             gff_compare = file("$projectDir/data/OPTIONAL_FILE")
             merge_gff = file("$projectDir/data/OPTIONAL_FILE")
             assembly_stats = file("$projectDir/data/OPTIONAL_FILE")
             use_ref_ann = false
-            results = Channel.empty()
+ 
         }
         if (jaffal_refBase){
                 gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
@@ -640,8 +653,6 @@ workflow pipeline {
 
        report = makeReport.out.report
 
-     
-       
        results = results.concat(makeReport.out.report)
        
        if (use_ref_ann){
@@ -676,6 +687,7 @@ workflow pipeline {
 
         results.concat(workflow_params.map{ [it, null]})
 
+       
     emit:
         results
 }

nextflow.config

@@ -115,7 +115,6 @@ manifest {
     version         = 'v0.4.2'
 }
 
-
 epi2melabs {
   tags = "isoforms, transcriptomics"
 }

subworkflows/reference_assembly.nf

@@ -12,18 +12,23 @@ process map_reads{
        tuple val(sample_id), path (fastq_reads), path(index), path(reference)
 
     output:
-       tuple val(sample_id), path("${sample_id}_reads_aln_sorted.bam"), emit: bam
+       tuple val(sample_id), 
+             path("${sample_id}_reads_aln_sorted.bam"), 
+             path("${sample_id}_reads_aln_sorted.bam.bai"),
+             emit: bam
        tuple val(sample_id), path("${sample_id}_read_aln_stats.tsv"), emit: stats
     script:
         def ContextFilter = """AlnContext: { Ref: "${reference}", LeftShift: -${params.poly_context},
         RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
         Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
+
+        def mm2_threads = Math.min(task.cpus - 3, 1)
     """
-    minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
+    minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
         | samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
-        | seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\
+        | seqkit bam -j 1 -x -T '${ContextFilter}' -\
-        | samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ;
+        | samtools sort --write-index -@ 1 -o "${sample_id}_reads_aln_sorted.bam##idx##${sample_id}_reads_aln_sorted.bam.bai" - ;
-    ((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j ${params.threads} - 2>&1)  | tee ${sample_id}_read_aln_stats.tsv ) || true
+    ((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j 1 - 2>&1)  | tee ${sample_id}_read_aln_stats.tsv ) || true
 
     if [[ -s "internal_priming_fail.tsv" ]];
         then