Fixed failing tests, added configs, and added pipeline test

.github/workflows/ci.yml

@@ -9,7 +9,6 @@ on:
       - checks_requested
     branches:
       - master
-      - dev
 
 env:
   NXF_ANSI_LOG: false

assets/samplesheet.csv

@@ -1,3 +1,5 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,replicate,group,fastq_1,fastq_2
+test1,rep1,group1,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz
+test1,rep2,group1,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz
+test2,rep1,group1,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz
+

main.nf

@@ -90,24 +90,6 @@ workflow {
     )
 }
 
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    COMPLETION EMAIL AND SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
-    }
-    NfcoreTemplate.summary(workflow, params, log)
-    if (params.hook_url) {
-        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
-    }
-}
-
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

modules/local/kneaddata/database/nextflow.config

@@ -0,0 +1,10 @@
+process {
+    withName: KNEADDATA_DATABASE {
+        publishDir = [
+            enabled: params.kneaddata_save_db,
+            path: { "${params.outdir}/ReadPreprocessing/kneaddata/database" },
+            mode: params.publish_dir_mode,
+            pattern: 'kneaddata_*/',
+        ]
+    }
+}

modules/local/kneaddata/kneaddata/nextflow.config

@@ -0,0 +1,17 @@
+process {
+    withName: KNEADDATA_KNEADDATA {
+        publishDir = [
+            [
+                path: { "${params.outdir}/ReadPreprocessing/kneaddata/kneaddata" },
+                mode: params.publish_dir_mode,
+                pattern: '*_kneaddata_paired_*.fastq.gz'
+            ],
+            [
+                path: { "${params.outdir}/ReadPreprocessing/kneaddata/kneaddata" },
+                mode: params.publish_dir_mode,
+                pattern: '*_kneaddata.log'
+            ]
+        ]
+        ext.args = params.kneaddata_options ? params.kneaddata_options : ""
+    }
+}

modules/local/kneaddata/kneaddata/tests/main.nf.test.snap

@@ -7,8 +7,8 @@
                         "id": "test"
                     },
                     [
-                        "test_kneaddata_paired_1.fastq.gz:md5,bc575548c0169cf3f12c38590060cbec",
-                        "test_kneaddata_paired_2.fastq.gz:md5,6dd6bd3bcb33e9dda68afa0c78a33b2d"
+                        "test_kneaddata_paired_1.fastq.gz:md5,acba94fdc94d1e4229beec12086a93af",
+                        "test_kneaddata_paired_2.fastq.gz:md5,7c8a08782ad6705eced33d11d5032859"
                     ]
                 ]
             ],
@@ -20,7 +20,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-24T10:06:32.04321443"
+        "timestamp": "2024-04-24T11:11:09.743832394"
     },
     "fastq.gz - stub": {
         "content": [
@@ -75,6 +75,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-24T10:06:43.652978972"
+        "timestamp": "2024-04-24T11:11:19.559542979"
     }
 }

modules/local/kneaddata/readcounts/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::kneaddata=0.12.0

modules/local/kneaddata/readcounts/nextflow.config

@@ -0,0 +1,9 @@
+process {
+    withName: KNEADDATA_READCOUNTS {
+        publishDir = [
+            path: { "${params.outdir}/ReadPreprocessing/kneaddata/readcounts" },
+            mode: params.publish_dir_mode,
+            pattern: '*_kneaddata_read_counts.tsv'
+        ]
+    }
+}

modules/local/metaphlan/sgbtogtdbprofile/nextflow.config

@@ -0,0 +1,9 @@
+process {
+    withName: METAPHLAN_SGBTOGTDBPROFILE {
+        publishDir = [
+            path: { "${params.outdir}/ReadTaxonomy/metaphlan/sgbtogtdbprofile" },
+            mode: params.publish_dir_mode,
+            pattern: '*_gtdb_profile.txt'
+        ]
+    }
+}

nextflow.config

@@ -12,24 +12,26 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                       = null
-    run_runmerging              = true
+    run_runmerging              = false
 
     // KneadData options
-    run_kneaddata               = true
+    run_kneaddata               = false
     kneaddata_db                = null
     kneaddata_db_version        = 'human_genome'
+    kneaddata_save_db           = false
     kneaddata_trimmomatic_path  = '/usr/local/share/trimmomatic-0.39-2'
     kneaddata_options           = null
 
     // MetaPhlAn options
-    run_metaphlan               = true
+    run_metaphlan               = false
     metaphlan_db                = null
     metaphlan_db_version        = null
+    metaphlan_save_db           = false
     metaphlan_options           = null
     metaphlan_sgb2gtbd_file     = "https://github.com/biobakery/MetaPhlAn/raw/master/metaphlan/utils/mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv"
 
     // HUMAnN options
-    run_humann                 = true
+    run_humann                 = false
     chocophlan_db_version       ='DEMO'
     uniref_db_version           ='DEMO_diamond'
     utility_mapping_version     ='DEMO'
@@ -250,9 +252,6 @@ manifest {
     doi             = ''
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {

subworkflows/local/fastq_read_preprocessing_kneaddata/nextflow.config

@@ -0,0 +1,3 @@
+includeConfig '../../../modules/local/kneaddata/database/nextflow.config'
+includeConfig '../../../modules/local/kneaddata/kneaddata/nextflow.config'
+includeConfig '../../../modules/local/kneaddata/readcounts/nextflow.config'