Merge pull request #56 from LaurenceKuhl/master

fix bug full_test

CHANGELOG.md

@@ -20,6 +20,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix warning "module used more than once" ([#25](https://github.com/nf-core/crisprseq/pull/25))
 - Remove profile `aws_tower`, update from nf-core/tools v2.9 to make full tests pass ([#50](https://github.com/nf-core/crisprseq/pull/50))
 - Remove `quay.io` from all containers ([#50](https://github.com/nf-core/crisprseq/pull/50))
+- Fix resources on test screening full ([#50](https://github.com/nf-core/crisprseq/pull/56))
+- Fix id in crisprcleanr-normalize ([#50](https://github.com/nf-core/crisprseq/pull/56))
 
 ## [v1.0 - Salted Hypatia](https://github.com/nf-core/crisprseq/releases/tag/1.0) - [02.02.2023]
 

conf/test_screening_full.config

@@ -14,15 +14,10 @@ params {
     config_profile_name        = 'Full test screening profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input             = 'https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/full_test/samplesheet_full.csv'
     analysis          = 'screening'
     crisprcleanr      = "Brunello_Library"
-    mle_design_matrix = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/full_test/*_vs_*.txt"
+    mle_design_matrix = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/full_test/drugA_drugB_vs_treatment.txt"
     library           = "https://raw.githubusercontent.com/nf-core/test-datasets/crisprseq/testdata/brunello_target_sequence.txt"
 }

workflows/crisprseq_screening.nf

@@ -10,7 +10,7 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 WorkflowCrisprseq.initialise(params, log)
 
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.multiqc_config, params.reference_fasta, params.library, params.mle_design_matrix ]
+def checkPathParamList = [ params.multiqc_config, params.reference_fasta, params.library]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
@@ -19,7 +19,7 @@ if (params.library) { ch_library = file(params.library) }
 if (params.crisprcleanr) { ch_crisprcleanr= Channel.value(params.crisprcleanr) }
 
 if(params.mle_design_matrix) {
-    Channel.fromPath(params.mle_design_matrix)
+    Channel.fromPath(params.mle_design_matrix,checkIfExists: true)
         .set { ch_design }
 }
 /*