Fix more whitespace issues from linting

genomic-medicine-sweden · Nov 28, 2024 · e92ae56 · e92ae56
1 parent 2b18c82
commit e92ae56
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Showing 12 changed files with 105 additions and 118 deletions.
diff --git a/.prettierignore b/.prettierignore
@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+LICENSE
diff --git a/Makefile b/Makefile
@@ -86,11 +86,11 @@
 #
 #    This also goes for command substitution, so rather than:
 #
-#    	echo "Lines in file:" $(wc -l somefile.txt)
+#        echo "Lines in file:" $(wc -l somefile.txt)
 #
 #    ... you would write:
 #
-#    	echo "Lines in file:" $$(wc -l somefile.txt)
+#        echo "Lines in file:" $$(wc -l somefile.txt)
 #
 # 2. Makefiles also use some special variables with special meaning, to access
 #    things like the output and input files:
@@ -119,9 +119,9 @@
 #  like so:
 #
 #  name_of_rule: dependency1 \
-#  		dependency2 \
-#  		dependency3 \
-#  		dependency4 \
+#      dependency2 \
+#      dependency3 \
+#      dependency4 \
 
 # ==============================================================================
 # Various definitions
@@ -140,9 +140,9 @@ MNT_ROOT := /$(shell readlink -f . | cut -d"/" -f2)
 INSTALL_LOG := "$(SCRIPT_DIR)/.install.log"
 
 define log_message
-	@echo "--------------------------------------------------------------------------------" | tee -a $(INSTALL_LOG);
-	@echo "$$(date "+%Y-%m-%d %H:%M:%S"): $1" | tee -a $(INSTALL_LOG);
-	@echo "--------------------------------------------------------------------------------" | tee -a $(INSTALL_LOG);
+    @echo "--------------------------------------------------------------------------------" | tee -a $(INSTALL_LOG);
+    @echo "$$(date "+%Y-%m-%d %H:%M:%S"): $1" | tee -a $(INSTALL_LOG);
+    @echo "--------------------------------------------------------------------------------" | tee -a $(INSTALL_LOG);
 endef
 
 # ==============================================================================
@@ -152,10 +152,10 @@ endef
 install: assets/databases/emu_database/species_taxid.fasta assets/databases/emu_database/taxonomy.tsv assets/databases/krona/taxonomy/taxonomy.tab
 
 assets/databases/emu_database/species_taxid.fasta: assets/databases/emu_database/species_taxid.fasta.gz
-	zcat $< > $@
+    zcat $< > $@
 
 assets/databases/emu_database/taxonomy.tsv: assets/databases/emu_database/taxonomy.tsv.gz
-	zcat $< > $@
+    zcat $< > $@
 
 assets/databases/krona/taxonomy/taxonomy.tab: assets/databases/krona/taxonomy/taxonomy.tab.gz
-	zcat $< > $@
+    zcat $< > $@
diff --git a/bin/generate_input.sh b/bin/generate_input.sh
@@ -6,8 +6,8 @@ trap 'exit_status="$?" && echo "Error occurred on line $LINENO: $BASH_COMMAND" &
 
 # Usage message
 if [ "$#" -ne 1 ]; then
-  echo "Usage: $0 <directory>"
-  exit 1
+    echo "Usage: $0 <directory>"
+    exit 1
 fi
 
 
@@ -20,15 +20,15 @@ directory=$(realpath "$directory")
 ls -1 "$directory"/*fastq.gz > "reads.txt"
 echo "sample,fastq_1,fastq_2" > "samplesheet_merged.csv"
 while IFS= read -r line; do
-  # Get the filename 
-  read1_n=$(basename "$line")
-  # Full path to forward read
-  read1_n_path="${directory}/${read1_n}"
-  # Entry name (everything in the filename before ".fastq.gz")
-  sample_n=$(echo "$read1_n" | sed  's/\.fastq\.gz//')
-  # Append to the sample_sheet.csv file
-  echo  "${sample_n},${read1_n_path}," >> "samplesheet_merged.csv"
-  echo
+    # Get the filename
+    read1_n=$(basename "$line")
+    # Full path to forward read
+    read1_n_path="${directory}/${read1_n}"
+    # Entry name (everything in the filename before ".fastq.gz")
+    sample_n=$(echo "$read1_n" | sed 's/\.fastq\.gz//')
+    # Append to the sample_sheet.csv file
+    echo "${sample_n},${read1_n_path}," >> "samplesheet_merged.csv"
+    echo
 done < "reads.txt"
 
 cat "./samplesheet_merged.csv"
@@ -37,4 +37,3 @@ echo "file saved as samplesheet_merged.csv"
 echo
 rm -f ./reads.txt
 echo "Script finished"
-
diff --git a/bin/merge_barcodes.sh b/bin/merge_barcodes.sh
@@ -4,8 +4,8 @@ trap 'exit_status="$?" && echo Failed on line: $LINENO at command: $BASH_COMMAND
 # if not 2 arguments passed, quit
 if [ $# -ne 2 ]
 then
- echo "arguments are missing to start script. 2 argumens are expected"
- exit 1
+    echo "arguments are missing to start script. 2 argumens are expected"
+    exit 1
 fi
 
 # arguments
@@ -15,22 +15,21 @@ fastq_pass_dir_out="$2"
 parent_directory=$(dirname "$fastq_pass_dir_out")
 
 if [ ! -d "$parent_directory" ]; then
-  echo "Parent directory for $fastq_pass_dir_out does not exist: $parent_directory"
-  exit 1
+    echo "Parent directory for $fastq_pass_dir_out does not exist: $parent_directory"
+    exit 1
 fi
 
 if [ ! -d "$fastq_pass_dir_out" ]; then
-  mkdir "$fastq_pass_dir_out"
-  echo "Directory created: $fastq_pass_dir_out"
+    mkdir "$fastq_pass_dir_out"
+    echo "Directory created: $fastq_pass_dir_out"
 else
-  echo "Directory already exists: $fastq_pass_dir_out"
+    echo "Directory already exists: $fastq_pass_dir_out"
 fi
 
 for i in "$fastq_pass_dir_in"/barcode* ; do
-  barcode_path=$(realpath "$i")
-  echo "barcode path $barcode_path"
-  barcode_name=$(basename "$barcode_path")
-  echo "barcode_name $barcode_name"
-  cat "$barcode_path/"*".fastq.gz" > "$fastq_pass_dir_out/${barcode_name}.fastq.gz"
+    barcode_path=$(realpath "$i")
+    echo "barcode path $barcode_path"
+    barcode_name=$(basename "$barcode_path")
+    echo "barcode_name $barcode_name"
+    cat "$barcode_path/"*".fastq.gz" > "$fastq_pass_dir_out/${barcode_name}.fastq.gz"
 done
-
diff --git a/conf/modules.config b/conf/modules.config
@@ -102,23 +102,23 @@ process {
         ]
     }
     withName: EMU_ABUNDANCE {
-         publishDir = [
+        publishDir = [
             [
-                 path: { "${params.outdir}/results" },
-                 mode: params.publish_dir_mode,
-                 pattern: '*{.tsv,txt}'
+                path: { "${params.outdir}/results" },
+                mode: params.publish_dir_mode,
+                pattern: '*{.tsv,txt}'
             ],
             [
-                 path: { "${params.outdir}/results" },
-                 mode: params.publish_dir_mode,
-                 pattern: '*{.sam}',
-                 enabled: params.keep_files,
+                path: { "${params.outdir}/results" },
+                mode: params.publish_dir_mode,
+                pattern: '*{.sam}',
+                enabled: params.keep_files,
             ],
             [
-                 path: { "${params.outdir}/results" },
-                 mode: params.publish_dir_mode,
-                 pattern: '*{.fa}',
-                 enabled: params.output_unclassified
+                path: { "${params.outdir}/results" },
+                mode: params.publish_dir_mode,
+                pattern: '*{.fa}',
+                enabled: params.output_unclassified
             ],
 
         ]
@@ -176,7 +176,4 @@ process {
             ]
         ]
     }
-
-
-
 }
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -321,14 +321,14 @@ class NfcoreTemplate {
         Map colors = logColours(monochrome_logs)
         String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
-              """\n
+            """\n
             ${dashedLine(monochrome_logs)}
-${colors.blue}                     _____ __  __  _____      __   __  _____
-${colors.blue}                    / ____|  \\/  |/ ____|    /_ | / / / ____|
-${colors.blue}                   | |  __| \\  / | (___ ______| |/ /_| (___
-${colors.blue}                   | | |_ | |\\/| |\\___ \\______| | '_ \\\\___ \\
-${colors.blue}                   | |__| | |  | |____) |     | | (_) |___) |
-${colors.blue}                    \\_____|_|  |_|_____/      |_|\\___/_____/
+            ${colors.blue}                     _____ __  __  _____      __   __  _____
+            ${colors.blue}                    / ____|  \\/  |/ ____|    /_ | / / / ____|
+            ${colors.blue}                   | |  __| \\  / | (___ ______| |/ /_| (___
+            ${colors.blue}                   | | |_ | |\\/| |\\___ \\______| | '_ \\\\___ \\
+            ${colors.blue}                   | |__| | |  | |____) |     | | (_) |___) |
+            ${colors.blue}                    \\_____|_|  |_|_____/      |_|\\___/_____/
 
 
             ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}

diff --git a/lib/WorkflowGmsemu.groovy b/lib/WorkflowGmsemu.groovy
@@ -13,10 +13,10 @@ class WorkflowGmsemu {
         genomeExistsError(params, log)
 
 
-   //     if (!params.fasta) {
-   //         log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
-   //         System.exit(1)
-   //     }
+    //     if (!params.fasta) {
+    //         log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+    //         System.exit(1)
+    //     }
     }
 
     //

diff --git a/modules/local/generate_input/main.nf b/modules/local/generate_input/main.nf
@@ -5,19 +5,19 @@ process GENERATE_INPUT {
 
     debug true //print to stdout. debugging
 
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9':
         'quay.io/biocontainers/python:3.9' }"
 
     input:
-       path(merged_files) 
+        path(merged_files)
 
     output:
-//    publishDir 'fastq_pass_merged', mode: 'move'
-      path '*amplesheet_merged.csv' , emit : sample_sheet_merged
+//      publishDir 'fastq_pass_merged', mode: 'move'
+        path '*amplesheet_merged.csv' , emit : sample_sheet_merged
     script:
     """
     generate_input.sh $merged_files

diff --git a/modules/local/merge_barcodes/main.nf b/modules/local/merge_barcodes/main.nf
@@ -2,28 +2,25 @@
 process MERGE_BARCODES {
     debug true //print to stdout
 
-
-
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9':
         'quay.io/biocontainers/python:3.9' }"
 
 
     input:
-      path('fastq_pass')
+        path('fastq_pass')
 
     output:
-//    publishDir 'fastq_pass_merged', mode: 'move'
+//      publishDir 'fastq_pass_merged', mode: 'move'
 //      path('*fastq.gz') , emit : fastq_files_merged
-      path('fastq_pass_merged/*fastq.gz') , emit : fastq_files_merged
-      path('fastq_pass_merged') , emit : fastq_dir_merged
-    
+        path('fastq_pass_merged/*fastq.gz') , emit : fastq_files_merged
+        path('fastq_pass_merged') , emit : fastq_dir_merged
+
     script:
     """
     merge_barcodes.sh $fastq_pass fastq_pass_merged
     """
 }
-
diff --git a/modules/local/merge_barcodes_samplesheet/main.nf b/modules/local/merge_barcodes_samplesheet/main.nf
@@ -2,30 +2,25 @@
 process MERGE_BARCODES_SAMPLESHEET {
     debug true //print to stdout. debugging
 
-
-
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9':
         'quay.io/biocontainers/python:3.9' }"
 
-
-
     input:
-     path('barcodes_samplesheet') 
-     path('fastq_pass')
-   
+    path('barcodes_samplesheet')
+    path('fastq_pass')
+
 
     output:
     // publishDir 'fastq_pass_merged', mode: 'move'
     path('fastq_pass_merged/*fastq.gz') , emit : fastq_files_merged
     path('fastq_pass_merged') , emit : fastq_dir_merged
-    
+
     script:
     """
     merge_barcodes_samplesheet.py $barcodes_samplesheet fastq_pass_merged $fastq_pass 
     """
 }
-
diff --git a/nextflow.config b/nextflow.config
@@ -13,7 +13,7 @@ params {
     input                      = null
     db                         = null
 
-//    reads                    = null
+    //reads                    = null
     seqtype                    = "map-ont"
     min_abundance              = 0.0001
     minimap_max_alignments     = 50
@@ -23,27 +23,27 @@ params {
     output_unclassified        = true
 
 
-   //
-   // porechop_abi
+    //
+    // porechop_abi
     adapter_trimming            = false
 
-   //
-   // filtlong filtering
+    //
+    // filtlong filtering
     quality_filtering          = true
     longread_qc_qualityfilter_minlength = 1200
     longread_qc_qualityfilter_maxlength = 1800
     longread_qc_qualityfilter_min_mean_q = 94
 
-    //Save the trimmed reads
+    // Save the trimmed reads
     save_preprocessed_reads = false
 
-    // krona
+    // Krona
     run_krona                  = true
     krona_taxonomy_tab         = "$projectDir/assets/databases/krona/taxonomy/taxonomy.tab"
 
     // For barcode folders
     merge_fastq_pass           = null
-    barcodes_samplesheet       = null    
+    barcodes_samplesheet       = null
 
     // References
     // MultiQC options
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,3 +10,4 @@ testing/ @@
     testing*
     *.pyc
     bin/
+    LICENSE