update blobtk naming

sanger-tol · Dec 21, 2023 · 45639a7 · 45639a7
1 parent 8ef790d
commit 45639a7
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Showing 8 changed files with 25 additions and 25 deletions.
diff --git a/bin/windowstats_input.py b/bin/windowstats_input.py
@@ -12,7 +12,7 @@ def parse_args(args=None):
     parser = argparse.ArgumentParser(description=Description)
     parser.add_argument("--freq", help="Frequence fasta windows input file", required=True)
     parser.add_argument("--mononuc", help="Mononucleotide fasta windows input file", required=True)
-    parser.add_argument("--mosdepth", help="Mosdepth coverage input file", nargs="+", required=True)
+    parser.add_argument("--depth", help="Depth coverage input file", nargs="+", required=True)
     parser.add_argument("--countbusco", help="BUSCO gene counts by region", required=True)
     parser.add_argument("--output", help="Output TSV file.", required=True)
     parser.add_argument("--version", action="version", version="%(prog)s 1.0.0")
@@ -24,15 +24,15 @@ def make_dir(path):
         os.makedirs(path, exist_ok=True)
 
 
-def merge_all(freq, mononuc, mosdepth, countbusco):
+def merge_all(freq, mononuc, depth, countbusco):
     freq_fw = pd.read_csv(freq, sep="\t")
     mononuc_fw = pd.read_csv(mononuc, sep="\t")
     combo_fw = freq_fw.merge(mononuc_fw).rename(
         columns={"ID": "sequence", "GC_prop": "gc", "Prop_Ns": "n", "N": "ncount"}
     )
 
     count_df = pd.read_csv(countbusco, sep="\t").rename(columns={"ID": "sequence"})
-    for f in mosdepth:
+    for f in depth:
         tag = os.path.basename(f).replace(".regions.bed.gz", "")
         cov_df = pd.read_csv(
             f,
@@ -52,7 +52,7 @@ def main(args=None):
     out_dir = os.path.dirname(args.output)
     make_dir(out_dir)
 
-    merge_all(args.freq, args.mononuc, args.mosdepth, args.countbusco).to_csv(args.output, sep="\t", index=False)
+    merge_all(args.freq, args.mononuc, args.depth, args.countbusco).to_csv(args.output, sep="\t", index=False)
 
 
 if __name__ == "__main__":

diff --git a/conf/modules.config b/conf/modules.config
@@ -74,7 +74,7 @@ process {
         ext.args = "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1"
     }
 
-    withName: "BLOBTOOLKIT_DEPTH" {
+    withName: "BLOBTK_DEPTH" {
         ext.args = "-s 1000"
     }
 
@@ -108,7 +108,7 @@ process {
         ]
     }
 
-    withName: "BLOBTOOLKIT_IMAGES" {
+    withName: "BLOBTK_IMAGES" {
         publishDir = [
             path: { "${params.outdir}/${blobdir.name}/" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/blobtoolkit/depth.nf → modules/local/blobtk/depth.nf b/modules/local/blobtoolkit/depth.nf → modules/local/blobtk/depth.nf
@@ -1,4 +1,4 @@
-process BLOBTOOLKIT_DEPTH {
+process BLOBTK_DEPTH {
     tag "${meta.id}"
     label 'process_single'
 
@@ -28,7 +28,7 @@ process BLOBTOOLKIT_DEPTH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        blobtoolkit: \$(btk --version | cut -d' ' -f2 | sed 's/v//')
+        blobtk: \$(blobtk --version | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/local/blobtoolkit/images.nf → modules/local/blobtk/images.nf b/modules/local/blobtoolkit/images.nf → modules/local/blobtk/images.nf
@@ -1,4 +1,4 @@
-process BLOBTOOLKIT_IMAGES {
+process BLOBTK_IMAGES {
     tag "${meta.id}_${plot}"
     label 'process_single'
 
@@ -32,7 +32,7 @@ process BLOBTOOLKIT_IMAGES {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        blobtoolkit: \$(btk --version | cut -d' ' -f2 | sed 's/v//')
+        blobtk: \$(blobtk --version | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/local/windowstats_input.nf b/modules/local/windowstats_input.nf
@@ -10,7 +10,7 @@ process WINDOWSTATS_INPUT {
     input:
     tuple val(meta), path(freq)
     tuple val(meta), path(mononuc)
-    tuple val(meta), path(mosdepth)
+    tuple val(meta), path(depth)
     tuple val(meta), path(countbusco)
 
     output:
@@ -27,7 +27,7 @@ process WINDOWSTATS_INPUT {
     windowstats_input.py \\
         --freq ${freq} \\
         --mononuc ${mononuc} \\
-        --mosdepth ${mosdepth} \\
+        --depth ${depth} \\
         --countbusco ${countbusco} \\
         --output ${prefix}.tsv \\
         ${args}

diff --git a/subworkflows/local/collate_stats.nf b/subworkflows/local/collate_stats.nf
@@ -28,7 +28,7 @@ workflow COLLATE_STATS {
     ch_versions = ch_versions.mix ( BLOBTOOLKIT_COUNTBUSCOS.out.versions.first() )
 
 
-    // Combine outputs from Fasta windows, mosdepth, and count BUSCO genes
+    // Combine outputs from Fasta windows, blobtk depth, and count BUSCO genes
     WINDOWSTATS_INPUT ( freq, mononuc, cov, BLOBTOOLKIT_COUNTBUSCOS.out.tsv )
     ch_versions = ch_versions.mix ( WINDOWSTATS_INPUT.out.versions.first() )
 

diff --git a/subworkflows/local/coverage_stats.nf b/subworkflows/local/coverage_stats.nf
@@ -2,11 +2,11 @@
 // Calculate genome coverage and statistics
 //
 
-include { SAMTOOLS_VIEW     } from '../../modules/nf-core/samtools/view/main'
-include { SAMTOOLS_INDEX    } from '../../modules/nf-core/samtools/index/main'
-include { BLOBTOOLKIT_DEPTH } from '../../modules/local/blobtoolkit/depth'
-include { FASTAWINDOWS      } from '../../modules/nf-core/fastawindows/main'
-include { CREATE_BED        } from '../../modules/local/create_bed'
+include { SAMTOOLS_VIEW  } from '../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
+include { BLOBTK_DEPTH   } from '../../modules/local/blobtk/depth'
+include { FASTAWINDOWS   } from '../../modules/nf-core/fastawindows/main'
+include { CREATE_BED     } from '../../modules/local/create_bed'
 
 
 workflow COVERAGE_STATS {
@@ -59,12 +59,12 @@ workflow COVERAGE_STATS {
 
 
     // Calculate coverage
-    BLOBTOOLKIT_DEPTH ( ch_bam_csi )
-    ch_versions = ch_versions.mix ( BLOBTOOLKIT_DEPTH.out.versions.first() )
+    BLOBTK_DEPTH ( ch_bam_csi )
+    ch_versions = ch_versions.mix ( BLOBTK_DEPTH.out.versions.first() )
 
 
     // Combining  regions_bed in single channel
-    BLOBTOOLKIT_DEPTH.out.bed
+    BLOBTK_DEPTH.out.bed
     | combine ( fasta )
     | map { meta, bed, meta2, fasta -> [ meta2, bed ] }
     | groupTuple ()

diff --git a/subworkflows/local/view.nf b/subworkflows/local/view.nf
@@ -3,7 +3,7 @@
 //
 
 include { BLOBTOOLKIT_SUMMARY } from '../../modules/local/blobtoolkit/summary'
-include { BLOBTOOLKIT_IMAGES  } from '../../modules/local/blobtoolkit/images'
+include { BLOBTK_IMAGES       } from '../../modules/local/blobtk/images'
 
 workflow VIEW {
     take:
@@ -26,12 +26,12 @@ workflow VIEW {
     //
     plots = [ "blob", "cumulative", "snail" ]
 
-    BLOBTOOLKIT_IMAGES ( blobdir, plots )
-    ch_versions = ch_versions.mix( BLOBTOOLKIT_IMAGES.out.versions )
+    BLOBTK_IMAGES ( blobdir, plots )
+    ch_versions = ch_versions.mix( BLOBTK_IMAGES.out.versions )
 
 
     emit:
     summary  = BLOBTOOLKIT_SUMMARY.out.json  // channel: [ val(meta), path(json) ]
-    images   = BLOBTOOLKIT_IMAGES.out.png    // channel: [ val(meta), path(png) ]
+    images   = BLOBTK_IMAGES.out.png         // channel: [ val(meta), path(png) ]
     versions = ch_versions                   // channel: [ versions.yml ]
 }