Merge pull request #74 from sanger-tol/minor_1_5_fixes

Minor fixes, update miniprot params and synteny path
sanger-tol · Mar 21, 2023 · cd99d56 · cd99d56
2 parents 5d9fad7 + 643a44c
commit cd99d56
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -20,7 +20,7 @@ process {
         ]
     }
 
-    withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED' {
+    withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|.*:.*:SYNTENY:MINIMAP2_ALIGN' {
         publishDir = [
             path: { "${params.outdir}/${task.process.tokenize(':')[-2].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
@@ -33,7 +33,7 @@ process {
     }
 
     withName: MINIPROT_ALIGN {
-        ext.args    = "-u --gff -j 1"
+        ext.args    = " --gff -j1 -ut16 --gff-delim='#' "
     }
 
     withName: '.*:.*:.*:(GEN_ALIGNMENTS|RNA_ALIGNMENTS|CDS_ALIGNMENTS):MINIMAP2_ALIGN' {
@@ -49,6 +49,10 @@ process {
         ext.prefix = { "${meta.id}_${meta.type}" }
     }
 
+    withName: '.*:.*:.*:PEP_ALIGNMENTS:BEDTOOLS_SORT' {
+        ext.prefix = { "${meta.id}_prot" }
+    }
+
     withName: '.*:.*:INSILICO_DIGEST:UCSC_BEDTOBIGBED' {
         ext.args        = { "-type=bed4+1 -extraIndex=length" }
         ext.prefix      = { "${meta.id}" }

diff --git a/modules/local/get_synteny_genomes.nf b/modules/local/get_synteny_genomes.nf
@@ -16,12 +16,12 @@ process GET_SYNTENY_GENOMES {
 
     script:
     """
-    if [ ! -d ${synteny_path}/${assembly_classT}/ ] || [ -z "\$(ls -A ${synteny_path}/${assembly_classT}/)" ]
+    if [ ! -d ${synteny_path}${assembly_classT}/ ] || [ -z "\$(ls -A ${synteny_path}${assembly_classT}/)" ]
     then
         echo "Directory is empty or doesn't exist"
         touch empty.fasta
     else
-        cp "${synteny_path}/${assembly_classT}/*.fasta" .
+        cp ${synteny_path}${assembly_classT}/*.fasta .
     fi
 
     cat <<-END_VERSIONS > versions.yml