Formatting and channel refactoring

sanger-tol · Nov 22, 2023 · 53b9d83 · 53b9d83
1 parent d2efbae
commit 53b9d83
Show file tree

Hide file tree

Showing 19 changed files with 77 additions and 86 deletions.
diff --git a/subworkflows/local/ancestral_gene.nf b/subworkflows/local/ancestral_gene.nf
@@ -10,10 +10,10 @@ include { UCSC_BEDTOBIGBED   } from '../../modules/nf-core/ucsc/bedtobigbed/main
 
 workflow ANCESTRAL_GENE {
     take:
-    busco_dir            // Channel: [val(meta),/path/to/busco/output/dir]
-    dot_genome           // Channel: [val(meta), [ datafile ]]
-    buscogene_as         // Channel val(dot_as location)
-    ancestral_table      // Channel val(ancestral_table location)
+    busco_dir            // Channel: tuple [val(meta),/path/to/busco/output/dir]
+    dot_genome           // Channel: tuple [val(meta), [ datafile ]]
+    buscogene_as         // Channel: val(dot_as location)
+    ancestral_table      // Channel: val(ancestral_table location)
 
     main:
     ch_versions             = Channel.empty()

diff --git a/subworkflows/local/busco_annotation.nf b/subworkflows/local/busco_annotation.nf
@@ -21,12 +21,12 @@ include { ANCESTRAL_GENE                } from './ancestral_gene'
 
 workflow BUSCO_ANNOTATION {
     take:
-    dot_genome           // channel: [val(meta), [ datafile ]]
-    reference_tuple      // channel: [val(meta), [ datafile ]]
-    lineageinfo          // channel: val(lineage_db)
-    lineagespath         // channel: val(/path/to/buscoDB)
-    buscogene_as         // channel: val(dot_as location)
-    ancestral_table      // channel: val(ancestral_table location)
+    dot_genome           // Channel: tuple [val(meta), [ datafile ]]
+    reference_tuple      // Channel: tuple [val(meta), [ datafile ]]
+    lineageinfo          // Channel: val(lineage_db)
+    lineagespath         // Channel: val(/path/to/buscoDB)
+    buscogene_as         // Channel: val(dot_as location)
+    ancestral_table      // Channel: val(ancestral_table location)
 
     main:
     ch_versions                 = Channel.empty()

diff --git a/subworkflows/local/gap_finder.nf b/subworkflows/local/gap_finder.nf
@@ -9,8 +9,8 @@ include { TABIX_BGZIPTABIX  } from '../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow GAP_FINDER {
     take:
-    reference_tuple     // Channel [ val(meta), path(fasta) ]
-    max_scaff_size      // val(size of largest scaffold in bp)
+    reference_tuple     // Channel: tuple [ val(meta), path(fasta) ]
+    max_scaff_size      // Channel: val(size of largest scaffold in bp)
 
     main:
     ch_versions     = Channel.empty()

diff --git a/subworkflows/local/gene_alignment.nf b/subworkflows/local/gene_alignment.nf
@@ -15,15 +15,15 @@ include { NUC_ALIGNMENTS as CDS_ALIGNMENTS  } from './nuc_alignments'
 
 workflow GENE_ALIGNMENT {
     take:
-    dot_genome          // Channel [ val(meta), path(file) ]
-    reference_tuple     // Channel [ val(meta), path(file) ]
-    reference_index     // Channel [ val(meta), path(file) ]
-    max_scaff_size      // Channel val(size of largest scaffold in bp)
-    alignment_datadir   // Channel val(geneset_dir)
-    alignment_genesets  // Channel val(geneset_id)
-    alignment_common    // Channel val(common_name) // Not yet in use
-    intron_size         // Channel val(50k)
-    as_files            // Channel [ val(meta), path(file) ]
+    dot_genome          // Channel: [ val(meta), path(file) ]
+    reference_tuple     // Channel: [ val(meta), path(file) ]
+    reference_index     // Channel: [ val(meta), path(file) ]
+    max_scaff_size      // Channel: val(size of largest scaffold in bp)
+    alignment_datadir   // Channel: val(geneset_dir)
+    alignment_genesets  // Channel: val(geneset_id)
+    alignment_common    // Channel: val(common_name) // Not yet in use
+    intron_size         // Channel: val(50k)
+    as_files            // Channel: [ val(meta), path(file) ]
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/generate_genome.nf b/subworkflows/local/generate_genome.nf
@@ -9,7 +9,7 @@ include { GET_LARGEST_SCAFF     } from '../../modules/local/get_largest_scaff'
 
 workflow GENERATE_GENOME {
     take:
-    reference_file  // Channel path(file)
+    reference_file  // Channel: path(file)
 
     main:
     ch_versions     = Channel.empty()

diff --git a/subworkflows/local/hic_mapping.nf b/subworkflows/local/hic_mapping.nf
@@ -28,17 +28,17 @@ include { PRETEXT_INGESTION as PRETEXT_INGEST_HIRES } from '../../subworkflows/l
 
 workflow HIC_MAPPING {
     take:
-    reference_tuple     // Channel [ val(meta), path( file )      ]
-    reference_index     // Channel [ val(meta), path( file )      ]
-    dot_genome          // Channel [ val(meta), path( datafile )  ]
-    hic_reads_path      // Channel [ val(meta), path( directory ) ]
-    assembly_id         // Channel val( id )
-    gap_file            // Channel [ val(meta), path( file )      ]
-    coverage_file       // Channel [ val(meta), path( file )      ]
-    logcoverage_file    // Channel [ val(meta), path( file )      ]
-    telo_file           // Channel [ val(meta), path( file )      ]
-    repeat_density_file // Channel [ val(meta), path( file )      ]
-    workflow_setting    // val( {RAPID | FULL } )
+    reference_tuple     // Channel: tuple [ val(meta), path( file )      ]
+    reference_index     // Channel: tuple [ val(meta), path( file )      ]
+    dot_genome          // Channel: tuple [ val(meta), path( datafile )  ]
+    hic_reads_path      // Channel: tuple [ val(meta), path( directory ) ]
+    assembly_id         // Channel: val( id )
+    gap_file            // Channel: tuple [ val(meta), path( file )      ]
+    coverage_file       // Channel: tuple [ val(meta), path( file )      ]
+    logcoverage_file    // Channel: tuple [ val(meta), path( file )      ]
+    telo_file           // Channel: tuple [ val(meta), path( file )      ]
+    repeat_density_file // Channel: tuple [ val(meta), path( file )      ]
+    workflow_setting    // Channel: val( { RAPID | FULL } )
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/insilico_digest.nf b/subworkflows/local/insilico_digest.nf
@@ -14,10 +14,10 @@ include { UCSC_BEDTOBIGBED              } from '../../modules/nf-core/ucsc/bedto
 
 workflow INSILICO_DIGEST {
     take:
-    sizefile        // Channel [ val(meta), path(my.genome_file) ]
-    reference          // Channel [ val(meta), path(reference_file) ]
-    ch_enzyme       // Channel val( "bspq1","bsss1","DLE1" )
-    dot_as          // Channel val(dot_as location)
+    sizefile        // Channel: tuple [ val(meta), path(my.genome_file) ]
+    reference       // Channel: tuple [ val(meta), path(reference_file) ]
+    ch_enzyme       // Channel: val( "bspq1","bsss1","DLE1" )
+    dot_as          // Channel: val(dot_as location)
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/kmer.nf b/subworkflows/local/kmer.nf
@@ -55,15 +55,6 @@ workflow KMER {
         }
         .set{ ch_reads_merged }
 
-    //
-    // LOGIC: PREPARE FASTK INPUT
-    //
-    CAT_CAT.out.file_out
-        .join( ch_reads_merged )
-        .map{ meta, reads_old, reads_new ->
-            reads_old.renameTo( reads_new );
-        }
-
     //
     // MODULE: COUNT KMERS
     //
@@ -74,18 +65,18 @@ workflow KMER {
     // LOGIC: PREPARE MERQURYFK INPUT
     //
     FASTK_FASTK.out.hist
-        .combine(FASTK_FASTK.out.ktab)
-        .combine(reference_tuple)
+        .combine( FASTK_FASTK.out.ktab )
+        .combine( reference_tuple )
         .map{ meta_hist, hist, meta_ktab, ktab, meta_ref, primary ->
-            tuple( meta_hist, hist, ktab, primary, [])
+            tuple( meta_hist, hist, ktab, primary, [] )
         }
         .set{ ch_merq }
 
     //
     // MODULE: USE KMER HISTOGRAM TO PRODUCE SPECTRA
     //
     MERQURYFK_MERQURYFK ( ch_merq )
-    ch_versions             = ch_versions.mix(MERQURYFK_MERQURYFK.out.versions.first())
+    ch_versions             = ch_versions.mix( MERQURYFK_MERQURYFK.out.versions.first() )
 
     emit:
     merquryk_completeness   = MERQURYFK_MERQURYFK.out.stats  // meta, stats
@@ -98,10 +89,10 @@ process GrabFiles {
     executor 'local'
 
     input:
-    tuple val(meta), path("in")
+    tuple val( meta ), path( "in" )
 
     output:
-    tuple val(meta), path("in/*.fasta.gz")
+    tuple val( meta ), path( "in/*.fasta.gz" )
 
     "true"
 }
diff --git a/subworkflows/local/longread_coverage.nf b/subworkflows/local/longread_coverage.nf
@@ -26,9 +26,9 @@ include { LONGREADCOVERAGESCALELOG2                 } from '../../modules/local/
 workflow LONGREAD_COVERAGE {
 
     take:
-    reference_tuple     // Channel: [ val(meta), file( reference_file ) ]
-    dot_genome          // Channel: [ val(meta), [ file( datafile ) ]   ]
-    reads_path          // Channel: [ val(meta), val( str )             ]
+    reference_tuple     // Channel: tuple [ val(meta), file( reference_file ) ]
+    dot_genome          // Channel: tuple [ val(meta), [ file( datafile ) ]   ]
+    reads_path          // Channel: tuple [ val(meta), val( str )             ]
 
     main:
     ch_versions             = Channel.empty()

diff --git a/subworkflows/local/nuc_alignments.nf b/subworkflows/local/nuc_alignments.nf
@@ -19,11 +19,11 @@ include { PUNCHLIST             } from './punchlist'
 
 workflow NUC_ALIGNMENTS {
     take:
-    reference_tuple     // Channel [ val(meta), path(file) ]
-    reference_index     // Channel [ val(meta), path(file) ]
-    nuc_files           // Channel [ val(meta), path(file) ]
-    dot_genome          // Channel [ val(meta), path(file) ]
-    intron_size         // Channel val(50k)
+    reference_tuple     // Channel: tuple [ val(meta), path(file) ]
+    reference_index     // Channel: tuple [ val(meta), path(file) ]
+    nuc_files           // Channel: tuple [ val(meta), path(file) ]
+    dot_genome          // Channel: tuple [ val(meta), path(file) ]
+    intron_size         // Channel: val(50k)
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/pep_alignments.nf b/subworkflows/local/pep_alignments.nf
@@ -12,9 +12,9 @@ include { EXTRACT_COV_IDEN      } from '../../modules/local/extract_cov_iden'
 
 workflow PEP_ALIGNMENTS {
     take:
-    reference_tuple     // Channel [ val(meta), path(file) ]
-    pep_files           // Channel [ val(meta), path(file) ]
-    max_scaff_size      // Channel val(size of largest scaffold in bp)
+    reference_tuple     // Channel: tuple [ val(meta), path(file) ]
+    pep_files           // Channel: tuple [ val(meta), path(file) ]
+    max_scaff_size      // Channel: tuple val(size of largest scaffold in bp)
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/pretext_ingestion.nf b/subworkflows/local/pretext_ingestion.nf
@@ -2,12 +2,12 @@ include { PRETEXT_GRAPH                                 } from '../../modules/lo
 
 workflow PRETEXT_INGESTION {
     take:
-    pretext_file        // tuple([sample_id], file)
-    gap_file            // tuple([sample_id], file)
-    coverage_file       // tuple([sample_id], file)
-    cov_log_file        // tuple([sample_id], file)
-    telomere_file       // tuple([sample_id], file)
-    repeat_cov_file     // tuple([sample_id], file)
+    pretext_file        // Channel: tuple([sample_id], file)
+    gap_file            // Channel: tuple([sample_id], file)
+    coverage_file       // Channel: tuple([sample_id], file)
+    cov_log_file        // Channel: tuple([sample_id], file)
+    telomere_file       // Channel: tuple([sample_id], file)
+    repeat_cov_file     // Channel: tuple([sample_id], file)
 
 
     main:

diff --git a/subworkflows/local/punchlist.nf b/subworkflows/local/punchlist.nf
@@ -8,8 +8,8 @@ include { PAF2BED               } from '../../modules/local/paf_to_bed'
 
 workflow PUNCHLIST {
     take:
-    reference_tuple // Channel [ val(meta), path(reference)]
-    merged_bam      // Channel [ val(meta), path(bam_file)]
+    reference_tuple // Channel: tuple [ val(meta), path(reference)]
+    merged_bam      // Channel: tuple [ val(meta), path(bam_file)]
 
     main:
     ch_versions         = Channel.empty()

diff --git a/subworkflows/local/repeat_density.nf b/subworkflows/local/repeat_density.nf
@@ -19,7 +19,7 @@ include { REPLACE_DOTS                      } from '../../modules/local/replace_
 
 workflow REPEAT_DENSITY {
     take:
-    reference_tuple     // Channel [ val(meta), path(file) ]
+    reference_tuple     // Channel: tuple [ val(meta), path(file) ]
     dot_genome
 
     main:

diff --git a/subworkflows/local/selfcomp.nf b/subworkflows/local/selfcomp.nf
@@ -18,11 +18,11 @@ include { BEDTOOLS_MERGE                 } from '../../modules/nf-core/bedtools/
 
 workflow SELFCOMP {
     take:
-    reference_tuple      // Channel [ val(meta), path(reference_file) ]
-    dot_genome           // Channel [ val(meta), [ path(datafile) ] ]
-    mummer_chunk         // Channel val( int )
-    motif_len            // Channel val( int )
-    selfcomp_as          // Channel val( dot_as location )
+    reference_tuple      // Channel: tuple [ val(meta), path(reference_file) ]
+    dot_genome           // Channel: tuple [ val(meta), [ path(datafile) ] ]
+    mummer_chunk         // Channel: val( int )
+    motif_len            // Channel: val( int )
+    selfcomp_as          // Channel: val( dot_as location )
 
     main:
     ch_versions             = Channel.empty()

diff --git a/subworkflows/local/synteny.nf b/subworkflows/local/synteny.nf
@@ -8,8 +8,8 @@ include { GET_SYNTENY_GENOMES   } from '../../modules/local/get_synteny_genomes'
 
 workflow SYNTENY {
     take:
-    reference_tuple     // Channel [ val(meta), path(file) ]
-    synteny_path        // Channel val(meta)
+    reference_tuple     // Channel: tuple [ val(meta), path(file) ]
+    synteny_path        // Channel: val(meta)
 
     main:
     ch_versions                 = Channel.empty()

diff --git a/subworkflows/local/telo_finder.nf b/subworkflows/local/telo_finder.nf
@@ -11,8 +11,8 @@ include { TABIX_BGZIPTABIX          } from '../../modules/nf-core/tabix/bgziptab
 workflow TELO_FINDER {
 
     take:
-    max_scaff_size      // val(size of largest scaffold in bp)
-    reference_tuple     // Channel [ val(meta), path(fasta) ]
+    max_scaff_size      // Channel: val(size of largest scaffold in bp)
+    reference_tuple     // Channel: tuple [ val(meta), path(fasta) ]
     teloseq
 
     main:

diff --git a/subworkflows/local/yaml_input.nf b/subworkflows/local/yaml_input.nf
@@ -4,7 +4,7 @@ import org.yaml.snakeyaml.Yaml
 
 workflow YAML_INPUT {
     take:
-    input_file  // input_yaml_from_commandline
+    input_file  // params.input
 
     main:
     ch_versions = Channel.empty()

diff --git a/workflows/treeval.nf b/workflows/treeval.nf
@@ -164,10 +164,10 @@ workflow TREEVAL {
     )
     ch_versions     = ch_versions.mix(GAP_FINDER.out.versions)
 
-    // //
-    // // SUBWORKFLOW: Takes reference file, .genome file, mummer variables, motif length variable and as
-    // //              file to generate a file containing sites of self-complementary sequnce.
-    // //
+    //
+    // SUBWORKFLOW: Takes reference file, .genome file, mummer variables, motif length variable and as
+    //              file to generate a file containing sites of self-complementary sequnce.
+    //
     SELFCOMP (
         YAML_INPUT.out.reference,
         GENERATE_GENOME.out.dot_genome,