Merge pull request #36 from ewels/change-filestructure

Restructure file hierarchy

.github/workflows/cutadapt.yml

@@ -2,7 +2,7 @@ name: cutadapt
 on:
   push: {}
   pull_request:
-    paths: tools/cutadapt/*
+    paths: software/cutadapt/*
 
 jobs:
   run_ci_test:
@@ -25,10 +25,10 @@ jobs:
 
       - name: Test module with paired-end data
         run: |
-          cd tools/cutadapt/test_paired/
+          cd software/cutadapt/test_paired/
           nextflow run . -ansi-log false
 
       - name: Test module with single-end data
         run: |
-          cd tools/cutadapt/test_single/
+          cd software/cutadapt/test_single/
           nextflow run . -ansi-log false

.github/workflows/docker.yml

@@ -5,8 +5,8 @@ on:
     branches: master
     # Only if a conda environment file or a docker build file has been updated
     paths:
-      - tools/*/environment.yml
-      - tools/*/Dockerfile
+      - software/*/environment.yml
+      - software/*/Dockerfile
 
 jobs:
   build_docker:
@@ -36,7 +36,7 @@ jobs:
             echo $TOOL
           done;
           echo '-----'
-          for d in tools/*; do
+          for d in software/*; do
             for TOOL in $TOOLS; do
               echo "$d -- $TOOL"
               if echo $d/ | grep -q "$TOOL"; then

.github/workflows/fastqc.yml

@@ -2,7 +2,7 @@ name: FastQC
 on:
   push: {}
   pull_request:
-    paths: tools/fastqc/*
+    paths: software/fastqc/*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/fastqc/test/ -ansi-log false
+    - run: nextflow run ./software/fastqc/test/ -ansi-log false

.github/workflows/samtools_index.yml

@@ -2,7 +2,7 @@ name: samtools index
 on:
   push: {}
   pull_request:
-    paths: tools/samtools/index*
+    paths: software/samtools/index*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/samtools/index/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/index/test/ -ansi-log false

.github/workflows/samtools_sort.yml

@@ -2,7 +2,7 @@ name: samtools sort
 on:
   push: {}
   pull_request:
-    paths: tools/samtools/sort*
+    paths: software/samtools/sort*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/samtools/sort/test/ -ansi-log false
+    - run: nextflow run ./software/samtools/sort/test/ -ansi-log false

.github/workflows/tcoffee.yml

@@ -2,7 +2,7 @@ name: tcoffee
 on:
   push: {}
   pull_request:
-    paths: tools/tcoffee/*
+    paths: software/tcoffee/*
 
 jobs:
   run_ci_test:
@@ -26,5 +26,5 @@ jobs:
 
     # Test the module
     - run: |
-        cd tools/tcoffee/test/
+        cd software/tcoffee/test/
         nextflow run . -ansi-log false

.github/workflows/trim_galore.yml

@@ -2,7 +2,7 @@ name: Trim Galore!
 on:
   push: {}
   pull_request:
-    paths: tools/trim_galore/*
+    paths: software/trim_galore/*
 
 jobs:
   run_ci_test:
@@ -20,4 +20,4 @@ jobs:
         sudo mv nextflow /usr/local/bin/
 
     # Test the module
-    - run: nextflow run ./tools/trim_galore/test/ -ansi-log false
+    - run: nextflow run ./software/trim_galore/test/ -ansi-log false

software/bwa/index/test/main.nf

@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../../../tests/functions/check_process_outputs.nf' params(params)
 include '../main.nf' params(params)
 
 // Define input channels

software/bwa/mem/test/main.nf

@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../../../../tests/functions/check_process_outputs.nf' params(params)
 include '../main.nf' params(params)
 
 reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'

software/fastq_screen/test/main.nf

@@ -12,7 +12,7 @@ if (params.verbose){
     println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args)
 }
 
-// TODO: include '../../../nf-core/module_testing/check_process_outputs.nf'
+// TODO: include '../../../tests/functions/check_process_outputs.nf'
 include '../main.nf'
 
 // Define input channels

software/fastqc/test/main.nf

@@ -6,7 +6,7 @@ params.fastqc_args = ''
 params.verbose = false
 
 // TODO: check the output files in some way
-// include '../../../nf-core/module_testing/check_process_outputs.nf'
+// include '../../../tests/functions/check_process_outputs.nf'
 include '../main.nf'
 
 // Define input channels

software/gatk/dict/test/main.nf

@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../../../tests/functions/check_process_outputs.nf' params(params)
 include '../main.nf' params(params)
 
 // Define input channels

software/htslib/tabix/test/main.nf

@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../../../tests/functions/check_process_outputs.nf' params(params)
 include '../main.nf' params(params)
 
 // Define input channels

software/multiqc/test/main.nf

@@ -5,7 +5,7 @@ params.outdir = "."
 params.verbose = false
 params.multiqc_args = ''
 
-// include '../../../nf-core/module_testing/check_process_outputs.nf'
+// include '../../../tests/functions/check_process_outputs.nf'
 include '../main.nf'
 
 if (params.verbose){

software/samtools/faidx/test/main.nf

@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 nextflow.preview.dsl = 2
-include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../../../tests/functions/check_process_outputs.nf' params(params)
 include '../main.nf' params(params)
 
 // Define input channels

software/tcoffee/test/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.preview.dsl = 2
 
-include check_output from  '../../../nf-core/module_testing/check_process_outputs.nf'
+include check_output from  '../../../tests/functions/check_process_outputs.nf'
 include tcoffee from '../main.nf'
 
 // Define input channels
@@ -13,8 +13,3 @@ workflow {
     tcoffee(fasta)
     // .check_output()
 }
-
-
-
-
-

software/trim_galore/test/main.nf

@@ -12,7 +12,7 @@ if (params.verbose){
 }
 
 // TODO: check the output files in some way
-// include '../../../nf-core/module_testing/check_process_outputs.nf'
+// include '../../../tests/functions/check_process_outputs.nf'
 include '../main.nf'  // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
 
 ch_read_files = Channel