Merge branch 'dev' into release-3.2.0

conf/modules_illumina.config

@@ -52,7 +52,7 @@ process {
             ]
         ]
     }
-    withName: 'CAT_FASTQ' {
+    withName: 'CAT_ILLUMINA_FASTQ' {
         publishDir = [
             [
                 path: { "${params.outdir}/fastq"},

modules.json

@@ -3,12 +3,6 @@
     "homePage": "https://github.com/CFIA-NCFAD/nf-flu",
     "repos": {
         "nf-core/modules": {
-            "blast/blastn": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "cat/fastq": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },

modules/local/blast_makeblastdb.nf

@@ -3,11 +3,11 @@ process BLAST_MAKEBLASTDB {
   tag "$fasta"
   label 'process_low'
 
-  conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
+  conda (params.enable_conda ? 'bioconda::blast=2.14.0' : null)
   if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-    container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--hf3cf87c_4'
+    container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
   } else {
-    container 'quay.io/biocontainers/blast:2.12.0--hf3cf87c_4'
+    container 'quay.io/biocontainers/blast:2.14.0--h7d5a4b4_1'
   }
 
   input:

modules/local/blastn.nf

@@ -0,0 +1,39 @@
+process BLAST_BLASTN {
+  tag "$meta.id"
+  label 'process_high'
+
+  conda (params.enable_conda ? 'bioconda::blast=2.14.0' : null)
+  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
+  } else {
+    container 'quay.io/biocontainers/blast:2.14.0--h7d5a4b4_1'
+  }
+
+  input:
+  tuple val(meta), path(fasta)
+  path  db
+
+  output:
+  tuple val(meta), path('*.blastn.txt'), emit: txt
+  path "versions.yml"                  , emit: versions
+
+  when:
+  task.ext.when == null || task.ext.when
+
+  script:
+  def args = task.ext.args ?: ''
+  def prefix = task.ext.prefix ?: "${meta.id}"
+  """
+  DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
+  blastn \\
+      -num_threads $task.cpus \\
+      -db \$DB \\
+      -query $fasta \\
+      $args \\
+      -out ${prefix}.blastn.txt
+  cat <<-END_VERSIONS > versions.yml
+  "${task.process}":
+      blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+  END_VERSIONS
+  """
+}

modules/local/cat_illumina_fastq.nf

@@ -0,0 +1,102 @@
+// modified nf-core/modules CAT_FASTQ
+// for paired end reads append 1:N:0:. or 2:N:0:. forward and reverse reads 
+// for compatability with IRMA assembly
+process CAT_ILLUMINA_FASTQ {
+  tag "$meta.id"
+  label 'process_single'
+
+  conda (params.enable_conda ? "conda-forge::perl" : null)
+  // use BLAST container here since it has Perl and is required by other
+  // processes in the pipeline
+  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    container 'https://depot.galaxyproject.org/singularity/blast:2.14.0--h7d5a4b4_1'
+  } else {
+    container 'quay.io/biocontainers/blast:2.14.0--h7d5a4b4_1'
+  }
+
+  input:
+  tuple val(meta), path(reads, stageAs: "input*/*")
+
+  output:
+  tuple val(meta), path("*.merged.fastq.gz"), emit: reads
+  path "versions.yml"                       , emit: versions
+
+  when:
+  task.ext.when == null || task.ext.when
+
+  script:
+  def args = task.ext.args ?: ''
+  def prefix = task.ext.prefix ?: "${meta.id}"
+  def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
+  def fqList = [] 
+  def fqgzList = []
+  readList.each { 
+    if (it ==~ /^.*\.(fastq|fq)$/) {
+      fqList << it
+    } else if (it ==~ /^.*\.(fastq|fq)\.gz$/) {
+      fqgzList << it
+    }
+  }
+  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(' ')} >> ${prefix}.merged.fastq.gz
+      fi
+
+      cat <<-END_VERSIONS > versions.yml
+      "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; 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 \\
+        >> ${prefix}_2.merged.fastq.gz
+      fi
+
+      cat <<-END_VERSIONS > versions.yml
+      "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+      END_VERSIONS
+      """
+    }
+  }
+}