Some more modules tweaks

nf-core · May 23, 2024 · 1284f55 · 1284f55
1 parent adbb1e2
commit 1284f55
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Showing 4 changed files with 35 additions and 1 deletion.
diff --git a/modules/local/convert_fasta.nf b/modules/local/convert_fasta.nf
@@ -18,7 +18,7 @@ process CONVERT_FASTA {
     task.ext.when == null || task.ext.when
 
     script:
-    prefix = task.ext.prefix ?: meta.id
+    def prefix = task.ext.prefix ?: meta.id
     """
     clustal2fasta.py $input_file ${prefix}.fa
 

diff --git a/modules/local/create_tcoffeetemplate.nf b/modules/local/create_tcoffeetemplate.nf
@@ -24,11 +24,21 @@ process CREATE_TCOFFEETEMPLATE {
         id=`echo \$structure | awk  {'gsub(".pdb", "", \$0); print'}`;
         echo -e ">"\$id "_P_" "\${id}" >> ${prefix}_template.txt;
     done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_template.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bash: \$(echo \$(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
+    END_VERSIONS
     """
 }
diff --git a/modules/local/dump_params.nf b/modules/local/dump_params.nf
@@ -33,10 +33,20 @@ process DUMP_PARAMS {
     skip_iqtree: ${skip_iqtree}
     skip_fastme: ${skip_fastme}
     END_PARAMS
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+    END_VERSIONS
     """
 
     stub:
     """
     touch params.yml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+    END_VERSIONS
     """
 }
diff --git a/modules/local/write_seqinfo.nf b/modules/local/write_seqinfo.nf
@@ -32,4 +32,18 @@ process WRITE_SEQINFO {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: meta.id
+    """
+    touch ${prefix}_id.txt
+    touch ${prefix}_exact.txt
+    touch ${prefix}_taxid.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }