Merge pull request #109 from jfy133/dev

Fix to PR #108

Author: apeltzer

README.md

@@ -55,7 +55,7 @@ nextflow pull nf-core/eager
 4. Set up your job with default parameters
 
 ```bash
-nextflow run nf-core -profile <docker/singularity/conda> --reads'*_R{1,2}.fastq.gz' --fasta '<REFERENCE.fasta'
+nextflow run nf-core -profile <docker/singularity/conda> --reads'*_R{1,2}.fastq.gz' --fasta '<REFERENCE>.fasta'
 ```
 
 5. See the overview of the run with under `<OUTPUT_DIR>/MultiQC/multiqc_report.html`

conf/multiqc_config.yaml

@@ -5,15 +5,15 @@ report_comment: >
 report_section_order:
     nf-core/eager-software-versions:
         order: -1000
-    fastqc:
-        after: 'nf-core/eager-software-versions'
-    adapterRemoval:
-        after: 'fastqc'
-    Samtools:
-        after: 'adapterRemoval'
-    dedup:
-        after: 'Samtools'
-    qualimap:
-        after: 'dedup'
-    preseq:
-        after: 'qualimap'
+top_modules:
+    - fastqc:
+        name: 'FastQC (raw)'
+        path_filters:
+            - '*_preAR_fastqc.zip'
+    - fastqc:
+        name: 'FastQC (trimmed)'
+        info: 'This section of the report shows FastQC results after adapter trimming.'
+        target: ''
+        path_filters:
+            - '*_postAR_fastqc.zip'
+

docs/configuration/adding_your_own.md

@@ -73,6 +73,9 @@ singularity.enabled = true
 process.container = "/path/to/nf-core-eager.simg"
 ```
 
+By default nextflow will store a singularity image in the working directory of a job. You can alternatively further specify a 'central' singularity cache to keep all singularity contains for a(ll) user(s). This can be
+done by either setting a central environmental variable `NXF_SINGULARITY_CACHEDIR` or specifying the location in a nextflow config file with `singularity.cacheDir`.
+
 ### Conda
 If you're not able to use Docker or Singularity, you can instead use conda to manage the software requirements.
 To use conda in your own config file, add the following:

docs/configuration/local.md

@@ -28,6 +28,11 @@ Many HPC environments are not able to run Docker due to security issues. [Singul
 ```bash
 nextflow run nf-core/eager -profile singularity --reads '<path to your reads>' --pairedEnd
 ```
+Note that by default nextflow will store the singularity container in the working directory of the nexflow run. To speed up jobs in the future, you can store your singularity containers in a specific cache directory, which can be specified by setting the environmental variable in your `bash_profile`. For example
+
+```
+NXF_SINGULARITY_CACHEDIR=/home/<user>/singularity
+```
 
 Additionally, it can use create images directly from dockerhub. To use the singularity image for a single run, use `-with-singularity 'docker://nfcore/eager'`. This will download the docker container from dockerhub and create a singularity image for you dynamically.
 

main.nf

@@ -738,14 +738,14 @@ process samtools_filter {
         """
         samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
         samtools index ${prefix}.filtered.bam
-        samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz"
+        samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz
         rm ${prefix}.unmapped.bam
         """
     } else if("${params.bam_discard_unmapped}" && "${params.bam_unmapped_type}" == "both"){
         """
         samtools view -h $bam | tee >(samtools view - -@ ${task.cpus} -f4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.unmapped.bam) >(samtools view - -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -o ${prefix}.filtered.bam)
         samtools index ${prefix}.filtered.bam
-        samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz"
+        samtools fastq -tn ${prefix}.unmapped.bam | pigz -p ${task.cpus} > ${prefix}.unmapped.fastq.gz
         """
     } else { //Only apply quality filtering, default
         """