Updated snapshots to reflect new nf-core modules

nf-core · Jan 17, 2024 · 0126a63 · 0126a63
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commit 0126a63
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Showing 35 changed files with 363 additions and 554 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -90,7 +90,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }},test_data --junitxml=test.xml
+          nf-test test --tag ${{ matrix.tags }} --profile test,${{ matrix.profile }},test_data --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

diff --git a/conf/test.config b/conf/test.config
@@ -15,26 +15,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
+    //max_cpus   = 2
+    //max_memory = '6.GB'
     max_time   = '6.h'
-
-    // Input data
-    input                         = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.multirun.csv'
-    centrifuge_db                 = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
-    kraken2_db                    = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
-    skip_krona                    = true
-    megahit_fix_cpu_1             = true
-    spades_fix_cpus               = 1
-    bowtie2_fix_cpu_1             = true
-    metabat2_fix_cpu_1            = true
-    maxbin2_fix_cpu_1             = true
-    concoct_fix_cpu_1             = true
-    binning_map_mode              = 'own'
-    min_length_unbinned_contigs   = 1000000
-    max_unbinned_contigs          = 2
-    busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
-    busco_clean                   = true
-    skip_gtdbtk                   = true
-    skip_concoct                  = true
 }
diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config
diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config
diff --git a/conf/test_bbnorm.config b/conf/test_bbnorm.config
diff --git a/conf/test_binrefinement.config b/conf/test_binrefinement.config
diff --git a/conf/test_busco_auto.config b/conf/test_busco_auto.config
diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config
diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
diff --git a/conf/test_hybrid_host_rm.config b/conf/test_hybrid_host_rm.config