fix parse_influenza_blast_results.py issue with Categorical type and …

…CAT_ILLUMINA_FASTQ versions.yml wonkiness
peterk87 · Jul 7, 2023 · 0d9db73 · 0d9db73
1 parent e38c9ca
commit 0d9db73
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Showing 4 changed files with 70 additions and 53 deletions.
diff --git a/bin/parse_influenza_blast_results.py b/bin/parse_influenza_blast_results.py
@@ -374,7 +374,7 @@ def report(flu_metadata, blast_results, excel_report, top, pident_threshold,
  ("Release_Date", pl.Categorical),
  ("Genus", pl.Categorical),
  ("Length", pl.UInt16),
- ("Genotype", pl.Categorical),
+ ("Genotype", str),
  ("Segment", pl.Categorical),
  ("Publications", str),
  ("Geo_Location", pl.Categorical),

diff --git a/conf/modules_illumina.config b/conf/modules_illumina.config
@@ -66,4 +66,14 @@ process {
  ]
  ]
  }
+
+ withName: 'SOFTWARE_VERSIONS' {
+ publishDir = [
+ [
+ path: { "${params.outdir}/pipeline_info" },
+ pattern: "software_versions.yml",
+ mode: params.publish_dir_mode
+ ]
+ ]
+ }
 }
diff --git a/modules/local/cat_illumina_fastq.nf b/modules/local/cat_illumina_fastq.nf
@@ -39,64 +39,71 @@ process CAT_ILLUMINA_FASTQ {
  }
  if (meta.single_end) {
  if (fqList.size >= 1 || fqgzList.size >= 1) {
-  """
-  touch ${prefix}.merged.fastq.gz
-  if [[ ${fqList.size} > 0 ]]; then
-  cat ${readList.join(' ')} | gzip -ck >> ${prefix}.merged.fastq.gz
-  fi
-  if [[ ${fqgzList.size} > 0 ]]; then
-  cat ${readList.join(' ')} >> ${prefix}.merged.fastq.gz
-  fi
+ """
+ touch ${prefix}.merged.fastq.gz
+ if [[ ${fqList.size} > 0 ]]; then
+ cat ${readList.join(' ')} | gzip -ck >> ${prefix}.merged.fastq.gz
+ fi
+ if [[ ${fqgzList.size} > 0 ]]; then
+ cat ${readList.join(' ')} >> ${prefix}.merged.fastq.gz
+ fi
 
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
- END_VERSIONS
- """
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ cat: \$(echo \$(cat --help 2>&1) | sed 's/ (.*//')
+ gzip: \$(echo \$(gzip --help 2>&1) | sed 's/ (.*//')
+ END_VERSIONS
+ """
  }
  } else {
  if (readList.size >= 2) {
  def read1 = []
  def read1gz = []
  def read2 = []
  def read2gz = []
- fqList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
- fqgzList.eachWithIndex{ v, ix -> ( ix & 1 ? read2gz : read1gz ) << v }
- """
- # append 1:N:0:. or 2:N:0:. to forward and reverse reads if "[12]:N:.*"
- # not present in the FASTQ header for compatability with IRMA assembly
- touch ${prefix}_1.merged.fastq.gz
- touch ${prefix}_2.merged.fastq.gz
- if [[ ${read1.size} > 0 ]]; then
- cat ${read1.join(' ')} \\
- | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
- | gzip -ck \\
- >> ${prefix}_1.merged.fastq.gz
- fi
- if [[ ${read1gz.size} > 0 ]]; then
- zcat ${read1gz.join(' ')} \\
- | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
- | gzip -ck \\
- >> ${prefix}_1.merged.fastq.gz
- fi
- if [[ ${read2.size} > 0 ]]; then
- cat ${read2.join(' ')} \\
- | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
- | gzip -ck \\
- >> ${prefix}_2.merged.fastq.gz
- fi
- if [[ ${read2gz.size} > 0 ]]; then
- zcat ${read2gz.join(' ')} \\
- | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
- | gzip -ck \\
- >> ${prefix}_2.merged.fastq.gz
- fi
+ fqList.eachWithIndex { v, ix -> ( ix & 1 ? read2 : read1 ) << v }
+ fqgzList.eachWithIndex { v, ix -> ( ix & 1 ? read2gz : read1gz ) << v }
+ // append 1:N:0:. or 2:N:0:. to forward and reverse reads if "[12]:N:.*"
+ // not present in the FASTQ header for compatability with IRMA assembly
+"""
+touch ${prefix}_1.merged.fastq.gz
 
- cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
- END_VERSIONS
- """
+touch ${prefix}_2.merged.fastq.gz
+
+if [[ ${read1.size} > 0 ]]; then
+ cat ${read1.join(' ')} \\
+ | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
+ | gzip -ck \\
+ >> ${prefix}_1.merged.fastq.gz
+fi
+
+if [[ ${read1gz.size} > 0 ]]; then
+ zcat ${read1gz.join(' ')} \\
+ | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 1:N:0:.\n"; } else { print "\$_"; }' \\
+ | gzip -ck \\
+ >> ${prefix}_1.merged.fastq.gz
+fi
+
+if [[ ${read2.size} > 0 ]]; then
+ cat ${read2.join(' ')} \\
+ | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
+ | gzip -ck \\
+ >> ${prefix}_2.merged.fastq.gz
+fi
+
+if [[ ${read2gz.size} > 0 ]]; then
+ zcat ${read2gz.join(' ')} \\
+ | perl -ne 'if (\$_ =~ /^@.*/ && !(\$_ =~ /^@.* [12]:N:.*/)){ chomp \$_; print "\$_ 2:N:0:.\n"; } else { print "\$_"; }' \\
+ | gzip -ck \\
+ >> ${prefix}_2.merged.fastq.gz
+fi
+
+cat <<-END_VERSIONS > versions.yml
+"${task.process}":
+ cat: \$(echo \$(cat --help 2>&1) | sed 's/ (.*//')
+ gzip: \$(echo \$(gzip --help 2>&1) | sed 's/ (.*//')
+END_VERSIONS
+"""
  }
  }
 }
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -78,13 +78,13 @@ workflow ILLUMINA {
  // Credit to nf-core/viralrecon. Source: https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/workflows/illumina.nf#L221
  // Concatenate FastQ files from same sample if required
  CAT_ILLUMINA_FASTQ(ch_input)
- ch_versions = ch_versions.mix(CAT_ILLUMINA_FASTQ.out.versions)
+ ch_versions = ch_versions.mix(CAT_ILLUMINA_FASTQ.out.versions.first().ifEmpty(null))
 
  IRMA(CAT_ILLUMINA_FASTQ.out.reads, irma_module)
- ch_versions = ch_versions.mix(IRMA.out.versions)
+ ch_versions = ch_versions.mix(IRMA.out.versions.first().ifEmpty(null))
 
  BLAST_BLASTN(IRMA.out.consensus, BLAST_MAKEBLASTDB.out.db)
- ch_versions = ch_versions.mix(BLAST_BLASTN.out.versions)
+ ch_versions = ch_versions.mix(BLAST_BLASTN.out.versions.first().ifEmpty(null))
 
  ch_blast = BLAST_BLASTN.out.txt.collect({ it[1] })
  SUBTYPING_REPORT(ZSTD_DECOMPRESS_CSV.out.file, ch_blast)