Add working basic test to begin

.github/workflows/ci.yml

@@ -48,3 +48,4 @@ jobs:
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+        # TODO Add test that runs with pre-downloaded and decompressed databases

conf/modules.config

@@ -26,6 +26,22 @@ process {
         ]
     }
 
+    withName: DATABASE_CHECK {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: UNTAR {
+       publishDir = [
+            path: { "${params.outdir}/databases" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: FASTQC {
         ext.args = '--quiet'
         ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }

conf/test.config

@@ -22,6 +22,12 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    outdir              = "./results"
+    // TODO replace with official once ready
+    databases           = 'https://raw.githubusercontent.com/jfy133/nf-core-test-datasets/taxprofiler/database.csv'
+    run_kraken2         = true
+    run_malt            = true
+    shortread_clipmerge = true
 
 }

subworkflows/local/input_check.nf

@@ -30,7 +30,7 @@ workflow INPUT_CHECK {
         .set { nanopore }
 
     parsed_samplesheet.fasta
-        .map { create_fasta_channels(it) }
+        .map { create_fasta_channel(it) }
         .dump(tag: "fasta_channel_init")
         .set { fasta }
 
@@ -42,7 +42,7 @@ workflow INPUT_CHECK {
 }
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
-def create_fastq_channels(LinkedHashMap row) {
+def create_fastq_channel(LinkedHashMap row) {
     // create meta map
     def meta = [:]
     meta.id                     = row.sample
@@ -74,7 +74,7 @@ def create_fastq_channels(LinkedHashMap row) {
 }
 
 // Function to get list of [ meta, fasta ]
-def create_fasta_channels(LinkedHashMap row) {
+def create_fasta_channel(LinkedHashMap row) {
     def meta = [:]
     meta.id                     = row.sample
     meta.run_accession          = row.run_accession

workflows/taxprofiler.nf

@@ -101,7 +101,9 @@ workflow TAXPROFILER {
     // PERFORM PREPROCESSING
     //
     if ( params.shortread_clipmerge ) {
-        SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq )
+        ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
+    } else {
+        ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
     }
 
     if ( params.longread_clip ) {
@@ -113,9 +115,10 @@ workflow TAXPROFILER {
     }
 
     //
-    // PERFORM RUN MERGING
+    // PERFORM SHORT READ RUN MERGING
+    // TODO: Check not necessary for long reads too?
     //
-    ch_processed_for_combine = SHORTREAD_PREPROCESSING.out.reads
+    ch_processed_for_combine = ch_shortreads_preprocessed
         .dump(tag: "prep_for_combine_grouping")
         .map {
             meta, reads ->
@@ -140,7 +143,7 @@ workflow TAXPROFILER {
     // COMBINE READS WITH POSSIBLE DATABASES
     //
 
-    // output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
+    // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
     ch_input_for_profiling = ch_reads_for_profiling
             .mix( ch_longreads_preprocessed )
             .combine(DB_CHECK.out.dbs)
@@ -152,7 +155,7 @@ workflow TAXPROFILER {
             }
 
     //
-    // PREP PROFILER INPUT CHANNELS ON PER TOOL BASIS
+    // PREPARE PROFILER INPUT CHANNELS
     //
 
     // We groupTuple to have all samples in one channel for MALT as database