Merge pull request #117 from jfy133/dev

MultiQC and Documentation Improvements

Author: apeltzer

conf/multiqc_config.yaml

@@ -2,27 +2,27 @@ report_comment: >
     This report has been generated by the <a href="https://github.com/nf-core/eager" target="_blank">nf-core/eager</a>
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/nf-core/eager" target="_blank">documentation</a>.
-report_section_order:
-    nf-core/eager-software-versions:
-        order: -1000
-    fastqc:
-        after: 'nf-core/eager-software-versions'
-        name: 'FastQC (raw)'
+top_modules:
+     - 'fastqc':
+        name: 'FastQC (pre-AdapterRemoval)'
         path_filters:
             - '*_fastqc.zip'
-    fastqc:
-        name: 'FastQC (trimmed)'
-        info: 'This section of the report shows FastQC results after adapter trimming.'
-        target: ''
-        path_filters:
-            - '*combined.prefixed_fastqc.zip'
-    adapterRemoval:
-        after: 'fastqc'
-    Samtools:
-        after: 'adapterRemoval'
-    dedup:
-        after: 'Samtools'
-    qualimap:
-        after: 'dedup'
-    preseq:
-        after: 'qualimap'
+        path_filters_exclude:
+             - '*.combined.prefixed_fastqc.zip'
+     - 'adapterRemoval'
+     - 'fastqc':
+         name: 'FastQC (post-AdapterRemoval)'
+         path_filters:
+             - '*.combined.prefixed_fastqc.zip'
+     - 'samtools'
+     - 'preseq'
+     - 'dedup'
+     - 'qualimap'
+     - 'damageprofiler'
+     - 'gatk'
+
+read_count_multiplier: 1
+read_count_prefix: ''
+read_count_desc: ''
+decimalPoint_format: '.'
+thousandsSep_format: ','

conf/shh.config

@@ -7,6 +7,7 @@
 
 singularity {
     enabled = true
+    cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/"
 }
 
 /*
@@ -29,6 +30,7 @@ process {
     }
 }
 
+
 params {
   max_memory = 734.GB
   max_cpus = 64

docs/configuration/adding_your_own.md

@@ -27,7 +27,6 @@ process {
   clusterOptions = '-A myproject'
 }
 ```
-
 ## Software Requirements
 To run the pipeline, several software packages are required. How you satisfy these requirements is essentially up to you and depends on your system. If possible, we _highly_ recommend using either Docker or Singularity.
 Please see the [`installation documentation`](../installation.md) for how to run using the below as a one-off. These instructions are about configuring a config file for repeated use.
@@ -84,6 +83,27 @@ To use conda in your own config file, add the following:
 process.conda = "$baseDir/environment.yml"
 ```
 
+## Software Caches
+
+Each new version of a pipeline downloaded and ran, will pull down a new image (docker/singularity)/collection (conda) of all the software required for the pipeline. By default this will be placed in the `work/` directory of an EAGER run. When running lots of pipeline jobs, this can slow down the pipeline (having to create a download a new environment each time) and take up a lot of hard-disk space (as each run has it's own duplicate of the environment).
+
+You can specify a central location for this using the `cacheDir` parameter [(see nextflow documentation)](https://www.nextflow.io/docs/latest/config.html). This can either be central for all users e.g.
+
+```
+singularity {
+  enabled = TRUE
+  cacheDir = '/<path>/<to/<cache_dir>/'
+}
+```
+
+Or if you give freedom to users as to which version they use
+
+```
+conda {
+  cacheDir = "/<path>/<to>/$USER/<cache_dir>"
+}
+```
+
 ## Job Resources
 #### Automatic resubmission
 Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with an error code of `143` (exceeded requested resources) it will automatically resubmit with higher requests (2 x original, then 3 x original). If it still fails after three times then the pipeline is stopped.