Remove pytest-workflow tests for modules covered by nf-test (#4521)

* Add first pass at the script * rmdir => rm -rf Never used rmdir before * Remove pytest-workflow tests for modules covered by nf-test * Use yq to remove tags * ci: Remove modules that didn't get their tags removed * Copy over fastqc tests todo * chore: Bump snapshot for fastqc
nf-core · Dec 4, 2023 · 3e8b0c1 · 3e8b0c1
1 parent 3aaf92f
commit 3e8b0c1
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diff --git a/.github/remove_pytest.bash b/.github/remove_pytest.bash
@@ -0,0 +1,12 @@
+#!/usr/bin/env cached-nix-shell
+#! nix-shell -i bash -p fd yq-go
+
+
+# Find modules that have a tests directory
+tested=$(fd main.nf.test modules/)
+
+for module in $tested; do
+    clean=$(dirname $module | sed 's|/tests||' | sed 's|modules/nf-core/||')
+    yq -i "del(.${clean})" tests/config/pytest_modules.yml
+    # rm -rf "tests/${clean}"
+done
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
@@ -38,4 +38,72 @@ nextflow_process {
             )
         }
     }
+// TODO
+// //
+// // Test with paired-end data
+// //
+// workflow test_fastqc_paired_end {
+//     input = [
+//                 [id: 'test', single_end: false], // meta map
+//                 [
+//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+//                 ]
+//             ]
+
+//     FASTQC ( input )
+// }
+
+// //
+// // Test with interleaved data
+// //
+// workflow test_fastqc_interleaved {
+//     input = [
+//                 [id: 'test', single_end: false], // meta map
+//                 file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)
+//             ]
+
+//     FASTQC ( input )
+// }
+
+// //
+// // Test with bam data
+// //
+// workflow test_fastqc_bam {
+//     input = [
+//                 [id: 'test', single_end: false], // meta map
+//                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+//             ]
+
+//     FASTQC ( input )
+// }
+
+// //
+// // Test with multiple samples
+// //
+// workflow test_fastqc_multiple {
+//     input = [
+//                 [id: 'test', single_end: false], // meta map
+//                 [
+//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+//                     file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
+//                     file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
+//                 ]
+//             ]
+
+//     FASTQC ( input )
+// }
+
+// //
+// // Test with custom prefix
+// //
+// workflow test_fastqc_custom_prefix {
+//     input = [
+//                 [ id:'mysample', single_end:true ], // meta map
+//                 file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+//             ]
+
+//     FASTQC ( input )
+// }
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -495,10 +495,6 @@ canu:
   - modules/nf-core/canu/**
   - tests/modules/nf-core/canu/**
 
-cat/fastq:
-  - modules/nf-core/cat/fastq/**
-  - tests/modules/nf-core/cat/fastq/**
-
 cdhit/cdhitest:
   - modules/nf-core/cdhit/cdhitest/**
   - tests/modules/nf-core/cdhit/cdhitest/**
@@ -1015,10 +1011,6 @@ fastk/merge:
   - modules/nf-core/fastk/merge/**
   - tests/modules/nf-core/fastk/merge/**
 
-fastqc:
-  - modules/nf-core/fastqc/**
-  - tests/modules/nf-core/fastqc/**
-
 fasttree:
   - modules/nf-core/fasttree/**
   - tests/modules/nf-core/fasttree/**
@@ -2971,10 +2963,6 @@ samtools/reheader:
   - modules/nf-core/samtools/reheader/**
   - tests/modules/nf-core/samtools/reheader/**
 
-samtools/sort:
-  - modules/nf-core/samtools/sort/**
-  - tests/modules/nf-core/samtools/sort/**
-
 samtools/view:
   - modules/nf-core/samtools/view/**
   - tests/modules/nf-core/samtools/view/**
@@ -3244,10 +3232,6 @@ smoove/call:
   - modules/nf-core/smoove/call/**
   - tests/modules/nf-core/smoove/call/**
 
-snakemake:
-  - modules/nf-core/snakemake/**
-  - tests/modules/nf-core/snakemake/**
-
 snapaligner/align:
   - modules/nf-core/snapaligner/align/**
   - tests/modules/nf-core/snapaligner/align/**

diff --git a/tests/modules/nf-core/abricate/run/main.nf b/tests/modules/nf-core/abricate/run/main.nf
diff --git a/tests/modules/nf-core/abricate/run/nextflow.config b/tests/modules/nf-core/abricate/run/nextflow.config
diff --git a/tests/modules/nf-core/abricate/run/test.yml b/tests/modules/nf-core/abricate/run/test.yml
diff --git a/tests/modules/nf-core/abricate/summary/main.nf b/tests/modules/nf-core/abricate/summary/main.nf
diff --git a/tests/modules/nf-core/abricate/summary/nextflow.config b/tests/modules/nf-core/abricate/summary/nextflow.config
diff --git a/tests/modules/nf-core/abricate/summary/test.yml b/tests/modules/nf-core/abricate/summary/test.yml
diff --git a/tests/modules/nf-core/art/illumina/main.nf b/tests/modules/nf-core/art/illumina/main.nf
diff --git a/tests/modules/nf-core/art/illumina/nextflow.config b/tests/modules/nf-core/art/illumina/nextflow.config
diff --git a/tests/modules/nf-core/art/illumina/test.yml b/tests/modules/nf-core/art/illumina/test.yml
diff --git a/tests/modules/nf-core/assemblyscan/main.nf b/tests/modules/nf-core/assemblyscan/main.nf
diff --git a/tests/modules/nf-core/assemblyscan/nextflow.config b/tests/modules/nf-core/assemblyscan/nextflow.config
diff --git a/tests/modules/nf-core/assemblyscan/test.yml b/tests/modules/nf-core/assemblyscan/test.yml