Merge pull request #245 from ggabernet/dev

Add missing module versions

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 - [#221](https://github.com/nf-core/airrflow/pull/221) Fixed bug arising when not providing `--index_file FALSE` for some input options not requiring index files.
 - [#239](https://github.com/nf-core/airrflow/pull/239) Implemented workaround for Slurm Sbatch file too large. We plan to revert when possible[#242](https://github.com/nf-core/airrflow/issues/242)
+- [#245](https://github.com/nf-core/airrflow/pull/245) Add missing module versions
 
 ### `Dependencies`
 

modules/local/reveal/add_meta_to_tab.nf

@@ -17,10 +17,17 @@ process ADD_META_TO_TAB {
     output:
     tuple val(meta), path("*meta-pass.tsv"), emit: tab // sequence tsv in AIRR format
     path("*_command_log.txt"), emit: logs //process logs
+    path "versions.yml", emit: versions
 
     script:
     """
-    # TODO: remove not relevant fields
     reveal_add_metadata.R --repertoire "${tab}" --metadata "${validated_input}" --input_id "${meta.id}" --outname "${meta.id}" > "${meta.id}_add-meta_command_log.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dplyr: \$(Rscript -e "library(dplyr); cat(paste(packageVersion('dplyr'), collapse='.'))")
+        optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
+        R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
+    END_VERSIONS
     """
 }

modules/local/reveal/filter_junction_mod3.nf

@@ -14,9 +14,18 @@ process FILTER_JUNCTION_MOD3 {
     output:
     tuple val(meta), path("*junction-pass.tsv"), emit: tab // sequence tsv in AIRR format
     path("*_command_log.txt"), emit: logs //process logs
+    path "versions.yml", emit: versions
 
     script:
     """
     reveal_mod_3_junction.R --repertoire $tab --outname ${meta.id} > "${meta.id}_jmod3_command_log.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        alakazam: \$(Rscript -e "library(alakazam); cat(paste(packageVersion('alakazam'), collapse='.'))")
+        optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
+        airr: \$(Rscript -e "library(airr); cat(paste(packageVersion('airr'), collapse='.'))")
+        R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
+    END_VERSIONS
     """
 }

modules/local/reveal/filter_quality.nf

@@ -14,10 +14,21 @@ process FILTER_QUALITY {
     output:
     tuple val(meta), path("*quality-pass.tsv"), emit: tab // sequence tsv in AIRR format
     path("*_command_log.txt"), emit: logs //process logs
+    path "versions.yml", emit: versions
 
     script:
-    // TODO: add to enchantr
     """
     reveal_filter_quality.R --repertoire $tab --outname ${meta.id} > "${meta.id}_fq_command_log.txt"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        alakazam: \$(Rscript -e "library(alakazam); cat(paste(packageVersion('alakazam'), collapse='.'))")
+        optparse: \$(Rscript -e "library(optparse); cat(paste(packageVersion('optparse'), collapse='.'))")
+        stringi: \$(Rscript -e "library(stringi); cat(paste(packageVersion('stringi'), collapse='.'))")
+        dplyr: \$(Rscript -e "library(dplyr); cat(paste(packageVersion('dplyr'), collapse='.'))")
+        airr: \$(Rscript -e "library(airr); cat(paste(packageVersion('airr'), collapse='.'))")
+        DT: \$(Rscript -e "library(DT); cat(paste(packageVersion('DT'), collapse='.'))")
+        R: \$(echo \$(R --version 2>&1) | awk -F' '  '{print \$3}')
+    END_VERSIONS
     """
 }

nextflow.config

@@ -86,11 +86,6 @@ params {
     igphyml="/usr/local/bin/igphyml"
     skip_lineage = false
 
-
-    // old bcellmagic options ----------------------
-    // Clustering parameters
-    // threshold_method = 'density'
-
     // -----------------------
     // reporting options
     // -----------------------

subworkflows/local/assembled_input_check.nf

@@ -10,7 +10,6 @@ workflow ASSEMBLED_INPUT_CHECK {
     miairr
     collapseby
     cloneby
-    //reassign
 
     main:
     // TODO: validate input should check that sample_ids are unique

subworkflows/local/vdj_annotation.nf

@@ -98,11 +98,11 @@ workflow VDJ_ANNOTATION {
     // - locus should match v_call chain
     // - seq alignment min length informative positions 200
     // - max 10% N nucleotides
-    // TODO: emit versions
     FILTER_QUALITY(
         ch_assigned_tab
     )
     ch_logs = ch_logs.mix(FILTER_QUALITY.out.logs)
+    ch_versions = ch_versions.mix(FILTER_QUALITY.out.versions.ifEmpty(null))
 
     if (params.productive_only) {
         CHANGEO_PARSEDB_SPLIT (
@@ -112,12 +112,13 @@ workflow VDJ_ANNOTATION {
         ch_versions = ch_versions.mix(CHANGEO_PARSEDB_SPLIT.out.versions.ifEmpty(null))
 
         // Apply filter: junction length multiple of 3
-        // TODO: Add to enchantr and emit versions?
         FILTER_JUNCTION_MOD3(
             CHANGEO_PARSEDB_SPLIT.out.tab
         )
         ch_logs = ch_logs.mix(FILTER_JUNCTION_MOD3.out.logs)
+        ch_versions = ch_versions.mix(FILTER_JUNCTION_MOD3.out.versions.ifEmpty(null))
         ch_repertoire = FILTER_JUNCTION_MOD3.out.tab.ifEmpty(null)
+
     } else {
         ch_repertoire = FILTER_QUALITY.out.tab.ifEmpty(null)
     }
@@ -126,8 +127,8 @@ workflow VDJ_ANNOTATION {
         ch_repertoire,
         ch_validated_samplesheet
     )
-    //TODO: emit versions
     ch_logs = ch_logs.mix(ADD_META_TO_TAB.out.logs)
+    ch_versions = ch_versions.mix(ADD_META_TO_TAB.out.versions.ifEmpty(null))
 
 
     emit:

workflows/airrflow.nf

@@ -9,7 +9,6 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 // Validate input parameters
 WorkflowAirrflow.initialise(params, log)
 
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
 // Check input path parameters to see if they exist
 def checkPathParamList = [ params.input, params.multiqc_config ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
@@ -45,7 +44,6 @@ ch_report_logo_img = Channel.fromPath(params.report_logo_img, checkIfExists: tru
 
 include { CHANGEO_CONVERTDB_FASTA as CHANGEO_CONVERTDB_FASTA_FROM_AIRR } from '../modules/local/changeo/changeo_convertdb_fasta'
 
-
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //