Fix snapshot due to name change of software files

nf-core · Mar 28, 2024 · 52cea03 · 52cea03
1 parent eef855d
commit 52cea03
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Showing 3 changed files with 1 addition and 22 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -68,9 +68,6 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
       - name: Install nf-test
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER

diff --git a/tests/test.nf.test b/tests/test.nf.test
@@ -31,7 +31,7 @@ nextflow_pipeline {
                         path("$outputDir/malt/malt_index/taxonomy.tre")
                     ).match()
                 },
-                { assert new File("$outputDir/pipeline_info/software_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
                 { assert path("$outputDir/malt/malt_index/table0.db").exists() },
                 { assert path("$outputDir/malt/malt_index/table0.idx").exists() },

diff --git a/workflows/createtaxdb.nf b/workflows/createtaxdb.nf
@@ -20,24 +20,6 @@ include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pi
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_createtaxdb_pipeline'
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES/SUBWORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~