Merge pull request #530 from nf-core/atrull-bb-comments

Addressing Austyn Trull's bouncy-basneji review comments
nf-core · Sep 24, 2024 · 3072502 · 3072502
2 parents b39da4b + e6a44cf
commit 3072502
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Showing 3 changed files with 13 additions and 15 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -314,20 +314,19 @@ profiles {
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
-    test                    { includeConfig 'conf/test.config'      }
-    test_full               { includeConfig 'conf/test_full.config' }
-    test_noprofiling        { includeConfig 'conf/test_noprofiling.config' }
-    test_nopreprocessing    { includeConfig 'conf/test_nopreprocessing.config' }
-    test_nothing            { includeConfig 'conf/test_nothing.config' }
-    test_motus              { includeConfig 'conf/test_motus.config' }
-    test_krakenuniq         { includeConfig 'conf/test_krakenuniq.config' }
-    test_malt               { includeConfig 'conf/test_malt.config' }
-    test_falco              { includeConfig 'conf/test_falco.config' }
-    test_fastp              { includeConfig 'conf/test_fastp.config' }
+    test                                 { includeConfig 'conf/test.config'                          }
+    test_full                            { includeConfig 'conf/test_full.config'                     }
+    test_noprofiling                     { includeConfig 'conf/test_noprofiling.config'              }
+    test_nopreprocessing                 { includeConfig 'conf/test_nopreprocessing.config'          }
+    test_nothing                         { includeConfig 'conf/test_nothing.config'                  }
+    test_motus                           { includeConfig 'conf/test_motus.config'                    }
+    test_krakenuniq                      { includeConfig 'conf/test_krakenuniq.config'               }
+    test_malt                            { includeConfig 'conf/test_malt.config'                     }
+    test_falco                           { includeConfig 'conf/test_falco.config'                    }
+    test_fastp                           { includeConfig 'conf/test_fastp.config'                    }
     test_alternativepreprocessing        { includeConfig 'conf/test_alternativepreprocessing.config' }
-    test_bbduk              { includeConfig 'conf/test_bbduk.config' }
-    test_prinseqplusplus    { includeConfig 'conf/test_prinseqplusplus.config' }
-
+    test_bbduk                           { includeConfig 'conf/test_bbduk.config'                    }
+    test_prinseqplusplus                 { includeConfig 'conf/test_prinseqplusplus.config'          }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
@@ -39,7 +39,6 @@ workflow LONGREAD_PREPROCESSING {
         FASTQC_PROCESSED ( ch_processed_reads )
         ch_versions      = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
-
     } else if (params.preprocessing_qc_tool == 'falco') {
         FALCO_PROCESSED ( ch_processed_reads )
         ch_versions      = ch_versions.mix( FALCO_PROCESSED.out.versions )

diff --git a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf b/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf
@@ -211,7 +211,7 @@ def toolCitationText() {
         "Long read preprocessing was performed with:",
         params.longread_adapterremoval_tool == "porechop_abi" ? "Porechop_ABI (Bonenfant et al. 2023)," : "",
         params.longread_adapterremoval_tool == "porechop" ? "Porechop (Wick et al. 2017)," : "",
-        params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)," : "",
+        params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)." : "",
         params.longread_filter_tool == "nanoq" ? "Nanoq (Steinig and Coin 2022)." : "",
     ].join(' ').trim()