Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test

conf/modules.config

@@ -281,7 +281,7 @@ process {
     }
 
     withName: MALT_RUN {
-        ext.args = { "${meta.db_params}" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
         // one run with multiple samples, so fix ID to just db name to ensure clean log name
         ext.prefix = { "${meta.db_name}" }
         publishDir = [
@@ -457,6 +457,13 @@ process {
     }
 
     withName: MOTUS_PROFILE {
+        ext.args = {
+            [
+                params.motus_remove_ncbi_ids ? "" : "-p",
+                params.motus_use_relative_abundance ? "" : "-c",
+                params.motus_save_mgc_read_counts ?  "-M ${task.ext.prefix}.mgc" : ""
+            ].join(',').replaceAll(','," ")
+            }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}/" },

conf/test.config

@@ -52,6 +52,7 @@ params {
 process {
     withName: MALT_RUN {
         maxForks = 1
+        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
     withName: MEGAN_RMA2INFO_TSV {
         maxForks = 1

conf/test_motus.config

@@ -44,5 +44,8 @@ params {
     run_diamond                           = false
     run_krakenuniq                        = false
     run_motus                             = true
+    motus_save_mgc_read_counts            = false
+    motus_remove_ncbi_ids                 = false
+    motus_use_relative_abundance          = false
     run_profile_standardisation           = true
 }

conf/test_nopreprocessing.config

@@ -46,5 +46,6 @@ params {
 process {
     withName: MALT_RUN {
         maxForks = 1
+        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
 }

conf/test_nothing.config

@@ -45,5 +45,6 @@ params {
 process {
     withName: MALT_RUN {
         maxForks = 1
+        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
 }

conf/test_pep.config

@@ -37,6 +37,7 @@ params {
 process {
     withName: MALT_RUN {
         maxForks = 1
+        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
     withName: MEGAN_RMA2INFO {
         maxForks = 1

lib/WorkflowMain.groovy

@@ -12,9 +12,9 @@ class WorkflowMain {
             // TODO nf-core: Add Zenodo DOI for pipeline after first release
             //"* The pipeline\n" +
             //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
-            "* The nf-core framework\n" +
+            '* The nf-core framework\n' +
-            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            '  https://doi.org/10.1038/s41587-020-0439-x\n\n' +
-            "* Software dependencies\n" +
+            '* Software dependencies\n' +
             "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
     }
 
@@ -53,15 +53,15 @@ class WorkflowMain {
             System.exit(0)
         }
 
+        // Print parameter summary log to screen
+
+        log.info paramsSummaryLog(workflow, params, log)
+
         // Validate workflow parameters via the JSON schema
         if (params.validate_params) {
             NfcoreSchema.validateParameters(workflow, params, log)
         }
 
-        // Print parameter summary log to screen
-
-        log.info paramsSummaryLog(workflow, params, log)
-
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
@@ -90,4 +90,5 @@ class WorkflowMain {
         }
         return null
     }
+
 }

modules.json

@@ -111,7 +111,7 @@
                     },
                     "malt/run": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
                     },
                     "megan/rma2info": {
                         "branch": "master",

modules/nf-core/malt/run/main.nf

@@ -2,14 +2,13 @@ process MALT_RUN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::malt=0.41" : null)
+    conda (params.enable_conda ? "bioconda::malt=0.61" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
+        'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
-        'quay.io/biocontainers/malt:0.41--1' }"
+        'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastqs)
-    val mode
     path index
 
     output:
@@ -38,7 +37,6 @@ process MALT_RUN {
         -o . \\
         $args \\
         --inFile ${fastqs.join(' ')} \\
-        -m $mode \\
         --index $index/ |&tee ${prefix}-malt-run.log
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/malt/run/meta.yml

@@ -28,10 +28,6 @@ input:
       type: file
       description: Input FASTQ files
       pattern: "*.{fastq.gz,fq.gz}"
-  - mode:
-      type: string
-      description: Program mode
-      pattern: "Unknown|BlastN|BlastP|BlastX|Classifier"
   - index:
       type: directory
       description: Index/database directory from malt-build

nextflow.config

@@ -145,7 +145,10 @@ params {
     diamond_save_reads         = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
 
     // mOTUs
-    run_motus                  = false
+    run_motus                       = false
+    motus_use_relative_abundance    = false
+    motus_remove_ncbi_ids           = false
+    motus_save_mgc_read_counts      = false
 
     // krona
     run_krona                  = false

nextflow_schema.json

@@ -464,6 +464,18 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
+                },
+                "motus_use_relative_abundance": {
+                    "type": "boolean",
+                    "description": "Turn on printing relative abundance instead of counts."
+                },
+                "motus_save_mgc_read_counts": {
+                    "type": "boolean",
+                    "description": "Turn on saving the mgc reads count."
+                },
+                "motus_remove_ncbi_ids": {
+                    "type": "boolean",
+                    "description": "Turn on removing NCBI taxonomic IDs."
                 }
             },
             "fa_icon": "fas fa-align-center"

subworkflows/local/profiling.nf

@@ -97,7 +97,7 @@ workflow PROFILING {
                                         db: it[2]
                                 }
 
-        MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
+        MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
 
         ch_maltrun_for_megan = MALT_RUN.out.rma6
                                 .transpose()