feat: create files summarizing annotation issues and failures

peterk87 · Jul 25, 2024 · fb0e4bf · fb0e4bf
1 parent 01f61e2
commit fb0e4bf
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Showing 5 changed files with 44 additions and 2 deletions.
diff --git a/conf/modules_illumina.config b/conf/modules_illumina.config
@@ -37,6 +37,17 @@ process {
  ]
  }
 
+ withName: 'VADR_SUMMARIZE_ISSUES' {
+ ext.args = ''
+ publishDir = [
+ [
+ path: { "${params.outdir}/annotation" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ]
+ }
+
  withName: 'POST_TABLE2ASN' {
  ext.args = ''
  publishDir = [

diff --git a/conf/modules_nanopore.config b/conf/modules_nanopore.config
@@ -255,6 +255,17 @@ process {
  ]
  }
 
+ withName: 'VADR_SUMMARIZE_ISSUES' {
+ ext.args = ''
+ publishDir = [
+ [
+ path: { "${params.outdir}/annotation" },
+ mode: params.publish_dir_mode,
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+ ]
+ }
+
  withName: 'POST_TABLE2ASN' {
  ext.args = ''
  publishDir = [

diff --git a/modules/local/vadr.nf b/modules/local/vadr.nf
@@ -29,3 +29,21 @@ process VADR {
  END_VERSIONS
  """
 }
+
+process VADR_SUMMARIZE_ISSUES {
+ executor 'local'
+ memory 100.MB
+
+ input:
+ path(vadr_output, stageAs: "input*/*")
+
+ output:
+ path('vadr-annotation-issues.txt'), emit: issues
+ path('vadr-annotation-failed-sequences.txt'), emit: failed
+
+ script:
+ """
+ cat input*/**/*.alt.list | awk 'NR == 1 || \$0 !~ /^#/' > vadr-annotation-issues.txt
+ cat input*/**/*.fail.list > vadr-annotation-failed-sequences.txt
+ """
+}
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -20,7 +20,7 @@ include { BLAST_MAKEBLASTDB } from '../modules/local/blast_makeblastdb'
 include { BLAST_BLASTN } from '../modules/local/blastn'
 include { CAT_ILLUMINA_FASTQ } from '../modules/local/cat_illumina_fastq'
 include { ZSTD_DECOMPRESS as ZSTD_DECOMPRESS_FASTA; ZSTD_DECOMPRESS as ZSTD_DECOMPRESS_CSV } from '../modules/local/zstd_decompress'
-include { VADR  } from '../modules/local/vadr'
+include { VADR; VADR_SUMMARIZE_ISSUES } from '../modules/local/vadr'
 include { PRE_TABLE2ASN; TABLE2ASN; POST_TABLE2ASN } from '../modules/local/table2asn'
 include { CUSTOM_DUMPSOFTWAREVERSIONS as SOFTWARE_VERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
 
@@ -92,6 +92,7 @@ workflow ILLUMINA {
  VADR.out.feature_table
  .combine(VADR.out.pass_fasta, by: 0)
  .set { ch_pre_table2asn }
+ VADR_SUMMARIZE_ISSUES(VADR.out.vadr_outdir.map { [it[1]] }.collect())
  PRE_TABLE2ASN(ch_pre_table2asn)
  ch_versions = ch_versions.mix(PRE_TABLE2ASN.out.versions)
  TABLE2ASN(PRE_TABLE2ASN.out.table2asn_input)

diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
@@ -32,7 +32,7 @@ include { BLAST_BLASTN as BLAST_BLASTN_IRMA } from '../modules
 include { BLAST_BLASTN as BLAST_BLASTN_CONSENSUS } from '../modules/local/blastn'
 include { BLAST_BLASTN as BLAST_BLASTN_CONSENSUS_REF_DB } from '../modules/local/blastn'
 include { CUSTOM_DUMPSOFTWAREVERSIONS as SOFTWARE_VERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
-include { VADR  } from '../modules/local/vadr'
+include { VADR; VADR_SUMMARIZE_ISSUES } from '../modules/local/vadr'
 include { PRE_TABLE2ASN; TABLE2ASN; POST_TABLE2ASN } from '../modules/local/table2asn'
 include { MULTIQC } from '../modules/local/multiqc'
 
@@ -247,6 +247,7 @@ workflow NANOPORE {
  VADR.out.feature_table
  .combine(VADR.out.pass_fasta, by: 0)
  .set { ch_pre_table2asn }
+ VADR_SUMMARIZE_ISSUES(VADR.out.vadr_outdir.map { [it[1]] }.collect())
  PRE_TABLE2ASN(ch_pre_table2asn)
  ch_versions = ch_versions.mix(PRE_TABLE2ASN.out.versions)
  TABLE2ASN(PRE_TABLE2ASN.out.table2asn_input)