Merge pull request #110 from nf-core/template_merge

Template merge

.github/workflows/branch.yml

@@ -34,4 +34,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-

.github/workflows/ci.yml

@@ -102,4 +102,4 @@ jobs:
 
       - name: Run pipeline with various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.profile_flags }}
+          nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.profile_flags }}

.github/workflows/linting.yml

@@ -68,4 +68,3 @@ jobs:
         with:
           name: linting-log-file
           path: lint_log.txt
-

.gitignore

@@ -102,4 +102,4 @@ results/
 .DS_Store
 tests/
 testing/
-*.pyc
+*.pyc

Dockerfile

@@ -12,4 +12,4 @@ RUN pip show sencha
 RUN sourmash info
 RUN bam2fasta info
 RUN sencha index --help
-RUN sencha translate --help
+RUN sencha translate --help

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

assets/email_template.html

@@ -51,4 +51,4 @@ <h3>Pipeline Configuration:</h3>
 </div>
 
 </body>
-</html>
+</html>

conf/base.config

@@ -80,4 +80,4 @@ params {
   max_memory = 128.GB
   max_cpus = 16
   max_time = 240.h
-}
+}

environment.yml

@@ -38,4 +38,4 @@ dependencies:
   - ripgrep=12.1.1
   - pip:
     - bam2fasta==1.0.8
-    - sencha==1.0.3
+    - sencha==1.0.3

main.nf

@@ -1049,20 +1049,20 @@ if ( have_nucleotide_input ) {
 
 if (params.subsample) {
   process subsample_input {
-  	tag "${id}_subsample"
-  	publishDir "${params.outdir}/seqtk/", mode: 'copy'
+    tag "${id}_subsample"
+    publishDir "${params.outdir}/seqtk/", mode: 'copy'
 
-  	input:
-  	set val(id), file(reads) from subsample_ch_reads_for_ribosomal_removal
+    input:
+    set val(id), file(reads) from subsample_ch_reads_for_ribosomal_removal
 
-  	output:
-  	set val(id), file("*_${params.subsample}.fastq.gz") into ch_reads_for_ribosomal_removal
+    output:
+    set val(id), file("*_${params.subsample}.fastq.gz") into ch_reads_for_ribosomal_removal
 
-  	script:
-  	read1 = reads[0]
-  	read2 = reads[1]
-  	read1_prefix = read1.simpleName
-  	read2_prefix = read2.simpleName
+    script:
+    read1 = reads[0]
+    read2 = reads[1]
+    read1_prefix = read1.simpleName
+    read2_prefix = read2.simpleName
 
     """
     seqtk sample -s100 ${read1} ${params.subsample} > ${read1_prefix}_${params.subsample}.fastq.gz
@@ -1631,4 +1631,4 @@ def checkHostname() {
             }
         }
     }
-}
+}

nextflow.config

@@ -216,4 +216,4 @@ def check_max(obj, type) {
       return obj
     }
   }
-}
+}