seqkit grep mulit

conf/modules.config

@@ -381,7 +381,7 @@ process {
                     path: { "${params.outdir}/assembly/polishing/intermediate/cluster/members" },
                     mode: params.publish_dir_mode,
                     enabled: params.save_intermediate_polishing,
-                    pattern: "*.fa.gz"
+                    pattern: "*.fa"
                 ]
             }
 
@@ -391,7 +391,7 @@ process {
                     path: { "${params.outdir}/assembly/polishing/intermediate/cluster/centroids" },
                     mode: params.publish_dir_mode,
                     enabled: params.save_intermediate_polishing,
-                    pattern: "*.fa.gz"
+                    pattern: "*.fa"
                 ]
             }
 

modules/local/seqkit_grep_multi.nf

@@ -0,0 +1,63 @@
+process SEQKIT_GREP_MULTI {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::seqkit=2.4.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.4.0--h9ee0642_0':
+        'biocontainers/seqkit:2.4.0--h9ee0642_0' }"
+
+    // Modified from original nf-core file
+    input:
+    tuple val(meta), path(txt_pattern_files)
+    path sequence
+
+    output:
+    tuple val(meta), path("*.{fa,fq}")  , emit: filter
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // fasta or fastq. Exact pattern match .fasta or .fa suffix with optional .gz (gzip) suffix
+    def suffix = task.ext.suffix ?: "${sequence}" ==~ /(.*f[astn]*a(.gz)?$)/ ? "fa" : "fq"
+
+    """
+    for file in ${txt_pattern_files.join(' ')};
+    do
+        prefix=\$( basename \${file} | sed 's/\\.[^.]*\$//' )
+        echo "Processing file: \${prefix} .."
+        seqkit \\
+            grep \\
+            $args \\
+            --threads $task.cpus \\
+            -f \${file} \\
+            ${sequence} \\
+            -o \$prefix.${suffix} \\
+            && echo "Done" || echo "Failed"
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // fasta or fastq. Exact pattern match .fasta or .fa suffix with optional .gz (gzip) suffix
+    def suffix = task.ext.suffix ?: "${sequence}" ==~ /(.*f[astn]*a(.gz)?$)/ ? "fa" : "fq"
+
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+    """
+}

subworkflows/local/clust_seq_extract.nf

@@ -1,10 +1,7 @@
 // modules
 include { CLUSTER_EXTRACT                       } from '../../modules/local/cluster_extract'
-include { SEQKIT_GREP as SEQKIT_GREP_MEMBERS    } from '../../modules/nf-core/seqkit/grep/main'
-include { SEQKIT_GREP as SEQKIT_GREP_CENTROIDS  } from '../../modules/nf-core/seqkit/grep/main'
-include { GUNZIP as GUNZIP_MEMBERS              } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_CENTROIDS            } from '../../modules/nf-core/gunzip/main'
-
+include { SEQKIT_GREP_MULTI as SEQKIT_GREP_MEMBERS    } from '../../modules/local/seqkit_grep_multi'
+include { SEQKIT_GREP_MULTI as SEQKIT_GREP_CENTROIDS  } from '../../modules/local/seqkit_grep_multi'
 
 workflow CLUST_SEQ_EXTRACT {
 
@@ -21,38 +18,24 @@ workflow CLUST_SEQ_EXTRACT {
     CLUSTER_EXTRACT(ch_clusters, cluster_method)
     ch_versions =  ch_versions.mix(CLUSTER_EXTRACT.out.versions.first())
 
-    // join with sequence data based on meta - transpose to a long format so we can split up the channels
-    CLUSTER_EXTRACT.out.members_centroids
-        .join(db_seq)
-        .transpose() //wide to long
-        .set { members_centroids_transposed }
-
-    // Update the meta data to include the cluster ID
-    ch_members_centroids = members_centroids_transposed.map { create_member_ref_channel(it) }
+    members_centroids = CLUSTER_EXTRACT.out.members_centroids
+    // [sample_meta, [members], [centroids] ]
 
-    // split up members, centroids and db for downstream processing
-    ch_members_centroids
-        .map { [ it[1] ] }
-        .set { ch_members }
-    ch_members_centroids
-        .map { [ it[2] ] }
-        .set { ch_centroids }
-    ch_members_centroids
-        .map { [ it[0], it[3] ] }
-        .set { ch_db_seq_anno }
+    ch_centroids  = members_centroids.map {meta, members, centroids -> [meta, centroids] }
+    ch_members    = members_centroids.map {meta, members, centroids -> [meta, members] }
 
-    SEQKIT_GREP_MEMBERS(ch_db_seq_anno,ch_members )
-    GUNZIP_MEMBERS(SEQKIT_GREP_MEMBERS.out.filter)
-
-    SEQKIT_GREP_CENTROIDS(ch_db_seq_anno,ch_centroids )
-    GUNZIP_CENTROIDS(SEQKIT_GREP_CENTROIDS.out.filter)
+    // extract members and centroids from db
 
+    SEQKIT_GREP_MEMBERS (ch_members, db_seq.map { it[1] } )
+    ch_versions =  ch_versions.mix(SEQKIT_GREP_MEMBERS.out.versions.first())
 
+    SEQKIT_GREP_CENTROIDS( ch_centroids, db_seq.map { it[1] })
     ch_versions =  ch_versions.mix(SEQKIT_GREP_CENTROIDS.out.versions.first())
-    ch_versions =  ch_versions.mix(GUNZIP_CENTROIDS.out.versions.first())
 
-    GUNZIP_CENTROIDS.out.gunzip
-        .join(GUNZIP_MEMBERS.out.gunzip, remainder: true)
+    SEQKIT_GREP_CENTROIDS.out.filter
+        .join(SEQKIT_GREP_MEMBERS.out.filter, remainder: true)
+        .transpose() //wide to long
+        .map { create_member_ref_channel(it) }
         .set { seq_centroids_members }
 
     emit:
@@ -62,19 +45,19 @@ workflow CLUST_SEQ_EXTRACT {
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
 def create_member_ref_channel(ArrayList row) {
-    members = row[1]
-    centroids = row[2]
-    sequence = row[3]
+    meta         = row[0]
+    centroids    = row[1]
+    members      = row[2]
 
-    sample             = String.valueOf(row[0].id) // just to make sure we don't pass by reference
-    regex              = (members =~ /.*\/.*_([0-9]+)_n([0-9]+)_members.txt/) // try and extract the correct cluster ID and size associated to the sample
-    cluster            = regex[0][1]
-    cluster_size       = regex[0][2] as int
-    id                 = "${sample}_${cluster}"
+    sample       = String.valueOf(meta.id) // just to make sure we don't pass by reference
+    regex        = (members =~ /.*\/.*_([0-9]+)_n([0-9]+)_members/) // try and extract the correct cluster ID and size associated to the sample
+    cluster      = regex[0][1]
+    cluster_size = regex[0][2] as int
+    id           = "${sample}_${cluster}"
 
-    new_meta = row[0] + [ id: id, cluster: cluster, cluster_size: cluster_size, sample: sample]
+    new_meta = meta + [ id: id, cluster: cluster, cluster_size: cluster_size, sample: sample]
 
-    def result = [ new_meta, members, centroids, sequence]
+    def result = [ new_meta, centroids, members]
     return result
 }
 

subworkflows/local/fastq_spades_trinity_megahit.nf

@@ -57,8 +57,6 @@ workflow FASTQ_SPADES_TRINITY_MEGAHIT  {
         .groupTuple()
         .set{ch_scaffolds_combined}
 
-    ch_scaffolds_combined.view()
-
     CAT_CAT(ch_scaffolds_combined)
     ch_versions = CAT_CAT.out.versions.first()