Merge pull request #686 from bigbio/updt_test_configs

🔧 update to fetch SDRF and FASTA files from maintained repo

Author: enryH

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/bigbio/quant
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/bigbio/quantms/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the bigbio/quantms _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If necessary, also make a PR on the bigbio/quantms _branch_ on the [bigbio/quantms-test-datasets](https://github.com/bigbio/quantms-test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

conf/tests/test_full_dia.config

@@ -25,7 +25,7 @@ params {
     outdir = './results_dia_full'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/dia_full/PXD004684.sdrf.tsv'
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata-aws/dia_full/PXD004684.sdrf.tsv'
     database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/REF_EColi_K12_UPS1_combined.fasta'
     min_pr_mz = 450
     max_pr_mz = 1080

conf/tests/test_full_lfq.config

@@ -25,8 +25,8 @@ params {
     outdir = "./results_lfq_full"
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/lfq_full/PXD001819.sdrf.tsv'
-    database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/lfq_full/yeast_2021_04_reviewed.fasta'
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata-aws/lfq_full/PXD001819.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata-aws/lfq_full/yeast_2021_04_reviewed.fasta'
     search_engines = "msgf,comet"
     add_decoys = true
     protein_level_fdr_cutoff = 0.01

conf/tests/test_full_tmt.config

@@ -25,8 +25,8 @@ params {
     outdir = "./results_iso_full"
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/tmt_full/PXD005486.sdrf.tsv'
-    database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/tmt_full/uniprot_E_coli_13spiked_reviewed_2021_04.fasta'
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata-aws/tmt_full/PXD005486.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata-aws/tmt_full/uniprot_E_coli_13spiked_reviewed_2021_04.fasta'
     search_engines = "comet,msgf"
     protein_level_fdr_cutoff = 0.01
     psm_level_fdr_cutoff = 0.01

conf/tests/test_latest_dia.config

@@ -40,7 +40,7 @@ process {
     }
 
     withLabel: diann {
-        container = 'ghcr.io/bigbio/diann:2.1.0' // This docker container is private in for quantms
+        container = 'ghcr.io/bigbio/diann:2.1.0' // This docker container is in a private registry for bigbio
     }
 
     resourceLimits = [

nextflow.config

@@ -56,12 +56,12 @@ params {
     shuffle_max_attempts                = 30
     shuffle_sequence_identity_threshold = 0.5
 
-    //// Peak picking if used
+    // Peak picking if used
     openms_peakpicking    = false
     peakpicking_inmemory  = false
     peakpicking_ms_levels = null // means all/auto
 
-    //// Conversion and mzml statistics flags
+    // Conversion and mzml statistics flags
     reindex_mzml          = true
     mzml_statistics       = false
     mzml_features         = false
@@ -271,7 +271,7 @@ params {
     help_full                  = false
     show_hidden                = false
     version                    = false
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/'
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     // Config options

nextflow_schema.json

@@ -1505,7 +1505,7 @@
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
+                    "default": "https://raw.githubusercontent.com/bigbio/quantms-test-datasets/",
                     "hidden": true
                 },
                 "trace_report_suffix": {

tests/nextflow.config

@@ -7,8 +7,8 @@
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
 params {
-    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/quantms'
+    modules_testdata_base_path = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/modules/data/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/refs/heads/quantms'
 }
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners