nf-core · CarsonJM · Feb 19, 2024 · Jan 24, 2024 · Jan 24, 2024 · Jan 24, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -104,7 +104,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --verbose --tag ${{ matrix.tags }} --profile test,"${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+          nf-test test --verbose --tag ${{ matrix.tags }} --profile "${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
 
       - uses: pcolby/tap-summary@v1
         with:

diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,7 @@ testing*
 *.pyc
 .nf-test*
 test.xml
+nf-test-checklist.csv
+*parallel-nf-test.sh
+nf-test-parallel/
+
diff --git a/conf/test.config b/conf/test.config
@@ -30,5 +30,3 @@ params {
     // Pipeline options
     publish_dir_mode            = 'symlink'
 }
-
-includeConfig './test_data.config'
diff --git a/conf/test_data.config b/conf/test_data.config
diff --git a/main.nf b/main.nf
@@ -28,7 +28,7 @@ Channel
     .fromSamplesheet("input")
     .multiMap { meta, fastq_1, fastq_2, fasta ->
         fastq_gz: [ meta, [ fastq_1, fastq_2 ] ]
-        fasta_gz: [ meta, [ fasta ] ]
+        fasta_gz: [ meta, fasta ]
     }
     .set { ch_input }
 

diff --git a/modules.json b/modules.json
@@ -112,29 +112,40 @@
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
+                    "pharokka/installdatabases": {
+                        "branch": "master",
+                        "git_sha": "10e88ef2f1f3ff012a2c9562de95c264006ebf21",
+                        "installed_by": ["modules"]
+                    },
+                    "pharokka/pharokka": {
+                        "branch": "master",
+                        "git_sha": "10e88ef2f1f3ff012a2c9562de95c264006ebf21",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff"
+                    },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "untar": {
@@ -148,12 +159,12 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["fastq_align_bowtie2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "fastq_align_bowtie2": {

diff --git a/modules/local/anicluster/anicalc/tests/main.nf.test b/modules/local/anicluster/anicalc/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     tag "modules"
     tag "modules_local"
     tag "anicluster"
-    tag "anicluster/anicalc"
+    tag "anicluster_anicalc"
 
 
     test("['modules_local']['blast_txt']") {

diff --git a/modules/local/anicluster/anicalc/tests/tags.yml b/modules/local/anicluster/anicalc/tests/tags.yml
@@ -1,2 +1,2 @@
-anicluster/anicalc:
+anicluster_anicalc:
   - modules/local/anicluster/anicalc/**
diff --git a/modules/local/anicluster/aniclust/tests/main.nf.test b/modules/local/anicluster/aniclust/tests/main.nf.test
@@ -6,18 +6,18 @@ nextflow_process {
     tag "modules"
     tag "modules_local"
     tag "anicluster"
-    tag "anicluster/aniclust"
+    tag "anicluster_aniclust"
 
 
-    test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv']") {
+    test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv']") {
 
         when {
             params {
                 outdir   = "$outputDir"
             }
             process {
                 """
-                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ],
+                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ],
                                                 [ file(params.test_data['modules_local']['ani_tsv'], checkIfExists: true ) ] ]
                 """
             }
@@ -31,7 +31,7 @@ nextflow_process {
         }
     }
 
-    test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub") {
+    test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub") {
 
         options "-stub"
 
@@ -41,7 +41,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ],
+                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ],
                                                 [ file(params.test_data['modules_local']['ani_tsv'], checkIfExists: true ) ] ]
                 """
             }

diff --git a/modules/local/anicluster/aniclust/tests/main.nf.test.snap b/modules/local/anicluster/aniclust/tests/main.nf.test.snap
diff --git a/modules/local/anicluster/aniclust/tests/tags.yml b/modules/local/anicluster/aniclust/tests/tags.yml
@@ -1,2 +1,2 @@
-anicluster/aniclust:
+anicluster_aniclust:
   - modules/local/anicluster/aniclust/**
diff --git a/modules/local/anicluster/extractreps/tests/main.nf.test b/modules/local/anicluster/extractreps/tests/main.nf.test
@@ -6,18 +6,18 @@ nextflow_process {
     tag "modules"
     tag "modules_local"
     tag "anicluster"
-    tag "anicluster/extractreps"
+    tag "anicluster_extractreps"
 
 
-    test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv']") {
+    test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv']") {
 
         when {
             params {
                 outdir   = "$outputDir"
             }
             process {
                 """
-                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ],
+                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ],
                                                 [ file(params.test_data['modules_local']['clusters_tsv'], checkIfExists: true ) ] ]
                 """
             }
@@ -31,7 +31,7 @@ nextflow_process {
         }
     }
 
-    test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub") {
+    test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub") {
 
         options "-stub"
 
@@ -41,7 +41,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ],
+                input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ],
                                                 [ file(params.test_data['modules_local']['clusters_tsv'], checkIfExists: true ) ] ]
                 """
             }

diff --git a/modules/local/anicluster/extractreps/tests/main.nf.test.snap b/modules/local/anicluster/extractreps/tests/main.nf.test.snap
diff --git a/modules/local/anicluster/extractreps/tests/tags.yml b/modules/local/anicluster/extractreps/tests/tags.yml
@@ -1,2 +1,2 @@
-anicluster/extractreps:
+anicluster_extractreps:
   - modules/local/anicluster/extractreps/**
diff --git a/modules/local/coverm/contig/nextflow.config b/modules/local/coverm/contig/nextflow.config
@@ -1,6 +1,11 @@
 process {
     withName: COVERM_CONTIG {
-        ext.args = "--methods $params.coverm_metrics"
+        ext.args   = [
+            "--methods $params.coverm_metrics",
+            "--min-read-aligned-length $params.coverm_min_read_alignment",
+            "--min-read-percent-identity $params.coverm_min_percent_identity",
+            "--min-read-aligned-percent $params.coverm_min_percent_read_aligned",
+        ].join(' ').trim()
         publishDir = [
                 path: { "${params.outdir}/VirusAbundance/coverm/contig" },
                 mode: params.publish_dir_mode,

diff --git a/modules/local/coverm/contig/tests/main.nf.test b/modules/local/coverm/contig/tests/main.nf.test
@@ -5,18 +5,18 @@ nextflow_process {
     process "COVERM_CONTIG"
     tag "modules"
     tag "modules_local"
-    tag "coverm/contig"
+    tag "coverm_contig"
 
 
-    test("['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam']") {
+    test("['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam']") {
 
         when {
             params {
                 outdir   = "$outputDir"
             }
             process {
                 """
-                input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_bam'], checkIfExists: true) ] ]
+                input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_paired_end_bam'], checkIfExists: true) ] ]
                 """
             }
         }
@@ -29,7 +29,7 @@ nextflow_process {
         }
     }
 
-    test("['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam'] - stub") {
+    test("['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam'] - stub") {
 
         options "-stub"
 
@@ -39,7 +39,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_bam'], checkIfExists: true) ] ]
+                input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_paired_end_bam'], checkIfExists: true) ] ]
                 """
             }
         }

diff --git a/modules/local/coverm/contig/tests/main.nf.test.snap b/modules/local/coverm/contig/tests/main.nf.test.snap
diff --git a/modules/local/coverm/contig/tests/tags.yml b/modules/local/coverm/contig/tests/tags.yml
@@ -1,2 +1,2 @@
-coverm/contig:
+coverm_contig:
   - modules/local/coverm/contig/**
diff --git a/modules/local/instrain/stb/tests/main.nf.test b/modules/local/instrain/stb/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "INSTRAIN_STB"
     tag "modules"
     tag "modules_local"
-    tag "instrain/stb"
+    tag "instrain_stb"
 
 
     test("['homo_sapiens']['genome']['genome_fasta']") {

diff --git a/modules/local/instrain/stb/tests/tags.yml b/modules/local/instrain/stb/tests/tags.yml
@@ -1,2 +1,2 @@
-instrain/stb:
+instrain_stb:
   - modules/local/instrain/stb/**
diff --git a/modules/local/mash/paste/tests/main.nf.test b/modules/local/mash/paste/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "MASH_PASTE"
     tag "modules"
     tag "modules_local"
-    tag "mash/paste"
+    tag "mash_paste"
 
 
     test("['modules_local']['mash_sketch1_msh'] & ['modules_local']['mash_sketch2_msh']") {

diff --git a/modules/local/mash/paste/tests/tags.yml b/modules/local/mash/paste/tests/tags.yml
@@ -1,2 +1,2 @@
-mash/paste:
+mash_paste:
   - modules/local/mash/paste/**
diff --git a/modules/local/prodigal/prodigalgv/environment.yml b/modules/local/prodigal/prodigalgv/environment.yml