Cleaned busco sample names and added files to multiqc

Plant-Food-Research-Open · Oct 8, 2024 · 1b09cba · 1b09cba
1 parent 8d348df
commit 1b09cba
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Showing 4 changed files with 25 additions and 5 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -34,3 +34,9 @@ module_order:
       info: "Annotation completeness statistics"
       path_filters_exclude:
         - "*seqkit.rmdup.fasta.txt"
+
+extra_fn_clean_exts:
+  - ".seqkit"
+  - ".rmdup"
+  - type: regex
+    pattern: "^short_summary\\.specific\\..*_odb10\\."
diff --git a/subworkflows/local/align_rnaseq.nf b/subworkflows/local/align_rnaseq.nf
@@ -76,6 +76,7 @@ workflow ALIGN_RNASEQ {
     ch_versions                 = ch_versions.mix(SAMTOOLS_CAT.out.versions.first())
 
     emit:
-    bam                         = ch_samtools_bam   // channel: [ [ id: target_assembly, single_end ], [ bam ] ]
-    versions                    = ch_versions       // channel: [ versions.yml ]
+    bam                         = ch_samtools_bam           // channel: [ [ id: target_assembly, single_end ], [ bam ] ]
+    star_log_final              = STAR_ALIGN.out.log_final  // channel: [ [ id: sample.on.assembly, single_end ], log ]
+    versions                    = ch_versions               // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/preprocess_rnaseq.nf b/subworkflows/local/preprocess_rnaseq.nf
@@ -117,7 +117,10 @@ workflow PREPROCESS_RNASEQ {
 
 
     emit:
-    trim_reads                      = ch_emitted_reads  // channel: [ [ id, single_end ], [ fq ] ]
-    reads_target                    = ch_reads_target   // channel: [ [ id, single_end ], assembly_id ]
-    versions                        = ch_versions       // channel: [ versions.yml ]
+    trim_reads                      = ch_emitted_reads                                  // channel: [ [ id, single_end ], [ fq ] ]
+    reads_target                    = ch_reads_target                                   // channel: [ [ id, single_end ], assembly_id ]
+    fastqc_raw_zip                  = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip    // channel: [ [ id, single_end ], zip ]
+    trim_json                       = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json         // channel: [ [ id, single_end ], json ]
+    fastqc_trim_zip                 = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip   // channel: [ [ id, single_end ], zip ]
+    versions                        = ch_versions                                       // channel: [ versions.yml ]
 }
diff --git a/workflows/genepal.nf b/workflows/genepal.nf
@@ -92,6 +92,12 @@ workflow GENEPAL {
 
     ch_trim_reads               = PREPROCESS_RNASEQ.out.trim_reads
     ch_reads_target             = PREPROCESS_RNASEQ.out.reads_target
+
+    ch_multiqc_files            = ch_multiqc_files
+                                | mix(PREPROCESS_RNASEQ.out.fastqc_raw_zip)
+                                | mix(PREPROCESS_RNASEQ.out.trim_json)
+                                | mix(PREPROCESS_RNASEQ.out.fastqc_trim_zip)
+
     ch_versions                 = ch_versions.mix(PREPROCESS_RNASEQ.out.versions)
 
     // SUBWORKFLOW: ALIGN_RNASEQ
@@ -103,6 +109,10 @@ workflow GENEPAL {
     )
 
     ch_rnaseq_bam               = ALIGN_RNASEQ.out.bam
+
+    ch_multiqc_files            = ch_multiqc_files
+                                | mix(ALIGN_RNASEQ.out.star_log_final)
+
     ch_versions                 = ch_versions.mix(ALIGN_RNASEQ.out.versions)
 
     // MODULE: PREPARE_EXT_PROTS