nf-core · maxulysse · Oct 13, 2023 · Oct 12, 2023 · Oct 12, 2023 · Oct 12, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,7 +11,6 @@ on:
       - master
       - dev
       - refactor
-      - nf-test
 
 env:
   NXF_ANSI_LOG: false

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Edmund Miller](https://github.com/Emiller88)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Harshil Patel](https://github.com/drpatelh)
+- [Lukas Forer](https://github.com/lukfor)
+- [James Fellows Yates](https://github.com/jfy133)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+- [Sateesh Peri](https://github.com/sateeshperi)
+- [Sebastian Schönherr](https://github.com/seppinho)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing
- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing
+- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing
+- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
+
 ### Enhancements & fixes
 
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
@@ -14,8 +35,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
+- [Davide Carlson](https://github.com/davidecarlson)
 - [Harshil Patel](https://github.com/drpatelh)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [MCMandR](https://github.com/MCMandR)
 - [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -37,7 +37,7 @@
 - [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/)
   > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337.
 
-## Software packaging/containerisation tools
+## Software packaging/containerisation/testing tools
 
 - [Anaconda](https://anaconda.com)
 
@@ -55,6 +55,8 @@
 
   > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
 
+- [nf-test](https://code.askimed.com/nf-test)
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: MULTIQC_MAPPINGS_CONFIG"
-    script "modules/local/multiqc_mappings_config/main.nf"
+    script "../main.nf"
     process "MULTIQC_MAPPINGS_CONFIG"
     tag "modules"
     tag "modules_local"

diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_FASTQ_FTP"
-    script "modules/local/sra_fastq_ftp/main.nf"
+    script "../main.nf"
     process "SRA_FASTQ_FTP"
     tag "modules"
     tag "modules_local"

diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_IDS_TO_RUNINFO"
-    script "modules/local/sra_ids_to_runinfo/main.nf"
+    script "../main.nf"
     process "SRA_IDS_TO_RUNINFO"
     tag "modules"
     tag "modules_local"

diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_MERGE_SAMPLESHEET"
-    script "modules/local/sra_merge_samplesheet/main.nf"
+    script "../main.nf"
     process "SRA_MERGE_SAMPLESHEET"
     tag "modules"
     tag "modules_local"

diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_RUNINFO_TO_FTP"
-    script "modules/local/sra_runinfo_to_ftp/main.nf"
+    script "../main.nf"
     process "SRA_RUNINFO_TO_FTP"
     tag "modules"
     tag "modules_local"

diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test process: SRA_TO_SAMPLESHEET"
-    script "modules/local/sra_to_samplesheet/main.nf"
+    script "../main.nf"
     process "SRA_TO_SAMPLESHEET"
     tag "modules"
     tag "modules_local"

diff --git a/nextflow.config b/nextflow.config
@@ -65,6 +65,16 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
+// Module specific configs
+includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
+
+// Workflow specific configs
+if (params.input_type == 'sra') {
+    includeConfig './workflows/sra/nextflow.config'
+} else if (params.input_type == 'synapse') {
+    includeConfig './workflows/synapse/nextflow.config'
+}
+
 // Load nf-core/fetchngs custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
 // try {
@@ -227,13 +237,6 @@ manifest {
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 
-// Module specific configs
-// Currently just dumpsoftwareversions
-includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config'
-
-// Workflow specific configs
-includeConfig 'workflows/nextflow.config'
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {

diff --git a/workflows/nextflow.config b/workflows/nextflow.config
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_default_parameters"
 
     test("Parameters: default") {

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_custom_ena_metadata_fields"
 
     test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {

diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_force_sratools_download"
 
     test("Parameters: --force_sratools_download") {

diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_atacseq"
 
     test("Parameters: --nf_core_pipeline atacseq") {

diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_rnaseq"
 
     test("Parameters: --nf_core_pipeline rnaseq") {

diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_taxprofiler"
 
     test("Parameters: --nf_core_pipeline taxprofiler") {

diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_nf_core_pipeline_viralrecon"
 
     test("Parameters: --nf_core_pipeline viralrecon") {

diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test
@@ -1,16 +1,16 @@
 nextflow_workflow {
 
     name "Test workflow: sra/main.nf"
-    script "workflows/sra/main.nf"
+    script "../main.nf"
     workflow "SRA"
+    tag "workflows"
+    tag "workflows_sra"
     tag "multiqc_mappings_config"
     tag "sra_fastq_ftp"
     tag "sra_ids_to_runinfo"
     tag "sra_merge_samplesheet"
     tag "sra_runinfo_to_ftp"
     tag "sra_to_samplesheet"
-    tag "workflows"
-    tag "workflows_sra"
     tag "sra_skip_fastq_download"
 
     test("Parameters: --skip_fastq_download") {
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,6 @@ on: @@
           - master
           - dev
           - refactor
-          - nf-test
     env:
       NXF_ANSI_LOG: false
@@ Expand Down @@