appears that sylph-tax is functional, isoquant taking far too long on transcriptomics data, further testing and polishing needed

Author: number-25

modules/local/sylph/get_tax_database/main.nf

@@ -0,0 +1,44 @@
+process GET_SYLPH_TAX_DB {
+    tag "SYLPH_TAX"
+    label 'process_low'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sylph-tax:1.8.0--pyhdfd78af_0' :
+        'biocontainers/sylph-tax:1.8.0--pyhdfd78af_0' }"
+
+    //input:
+    //val outpath
+
+    output:
+    path "tax_db"       , emit: sylph_tax_db
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    //def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}"
+
+    """
+    mkdir tax_db
+    sylph-tax download --download-to tax_db
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph_tax: \$(sylph-tax --version | cut -d" " -f2)
+    END_VERSIONS
+    """
+
+/*    stub:
+    //def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}"
+
+    """
+    touch *.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sylph_tax: \$(sylph-tax --version | cut -d" " -f2)
+    END_VERSIONS
+    """
+*/
+}

modules/local/sylph/get_tax_database/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'GET_SYLPH_TAX_DB' {
+        publishDir = [
+        path: { "${params.outdir}/profile_unmapped_reads/sylph" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

modules/local/sylph/profile/nextflow.config

@@ -1,5 +1,5 @@
 process {
-    withName: 'SYLPH_PREPARE_REFERENCE' {
+    withName: 'SYLPH_PROFILE' {
         publishDir = [
         path: { "${params.outdir}/profile_unmapped_reads/sylph" },
         //mode: params.publish_dir_mode

modules/local/sylph/tax/main.nf

@@ -8,30 +8,32 @@ process SYLPH_TAX {
 
     input:
     tuple val(meta), path(sylph_profile)
+    path database
     val database_name
 
     output:
-    tuple val(meta), path("*.sylphmpa")     , emit: sylph_tax
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("*.sylphmpa") , optional: true , emit: sylph_tax
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}_${meta.replicate}"
 
-    """
-    sylph-tax download --download-to .
 
-    sylph-tax taxprof \\
+    """
+    sylph-tax \\
+        --no-config \\
+        --taxonomy-dir $database \\
+        taxprof \\
         $sylph_profile \\
-        --taxonomy-dir !PWD \\
         -t $database_name \\
         -o ${prefix}_sylph_tax.sylphmpa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sylph_profile: \$(sylph-tax --version | cut -d" " -f2')
+        sylph_tax: \$(sylph-tax --version | cut -d" " -f2)
     END_VERSIONS
     """
 
@@ -42,7 +44,7 @@ process SYLPH_TAX {
     touch ${prefix}_sylph_tax.sylphmpa
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sylph_profile: \$(sylph-tax --version | cut -d" " -f2')
+        sylph_tax: \$(sylph-tax --version | cut -d" " -f2)
     END_VERSIONS
     """
 }

modules/local/sylph/tax/nextflow.config

@@ -0,0 +1,8 @@
+process {
+    withName: 'SYLPH_TAX' {
+        publishDir = [
+        path: { "${params.outdir}/profile_unmapped_reads/sylph" },
+        //mode: params.publish_dir_mode
+        ]
+    }
+}

subworkflows/local/profile_unmapped_reads/main.nf

@@ -1,5 +1,6 @@
 //include { SYLPH_PREPARE_REFERENCE   } from '../../../modules/local/sylph/prepare_reference'
 include { SYLPH_PROFILE             } from '../../../modules/local/sylph/profile'
+include { GET_SYLPH_TAX_DB          } from '../../../modules/local/sylph/get_tax_database'
 include { SYLPH_TAX                 } from '../../../modules/local/sylph/tax'
 
 workflow PROFILE_UNMAPPED_READS {
@@ -13,12 +14,13 @@ workflow PROFILE_UNMAPPED_READS {
 
     ch_versions = Channel.empty()
 
-    //ch_sylph_database = SYLPH_PREPARE_REFERENCE.out.database
-
     SYLPH_PROFILE( unmapped_reads, sylph_database )
     ch_sylph_profile = SYLPH_PROFILE.out.sylph_profile
 
-    SYLPH_TAX( ch_sylph_profile, sylph_database_name )
+    GET_SYLPH_TAX_DB()
+    ch_sylph_tax_db = GET_SYLPH_TAX_DB.out.sylph_tax_db
+
+    SYLPH_TAX( ch_sylph_profile, ch_sylph_tax_db, sylph_database_name )
     ch_sylph_tax = SYLPH_TAX.out.sylph_tax
 
     emit: