Merge pull request #594 from nf-core/patch-2.2.1

Patch 2.2.1

Author: jfy133

.dockstore.yml

@@ -4,9 +4,6 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch.
 
 on:
-  push:
-    branches:
-      - master
   workflow_dispatch:
 
 jobs:

.github/workflows/awstest.yml

@@ -34,13 +34,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/eager:2.2.0
+        run: docker build --no-cache . -t nfcore/eager:2.2.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.2.0
+          docker tag nfcore/eager:dev nfcore/eager:2.2.1
 
       - name: Install Nextflow
         run: |

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.10.2
+FROM nfcore/base:1.11
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"
 
@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.2.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.2.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.2.0 > nf-core-eager-2.2.0.yml
+RUN conda env export --name nf-core-eager-2.2.1 > nf-core-eager-2.2.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

CHANGELOG.md

@@ -60,6 +60,8 @@
 
 <!-- /TOC -->
 
+## Introduction
+
 ## Running the pipeline
 
 ### Quick Start
@@ -735,6 +737,10 @@ If you want to use pre-existing `bwa index` indices, please supply the
 nf-core/eager will automagically detect the index files by searching for the
 FASTA filename with the corresponding `bwa` index file suffixes.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash
@@ -756,6 +762,10 @@ If you want to use pre-existing `bt2 index` indices, please supply the
 nf-core/eager will automagically detect the index files by searching for the
 FASTA filename with the corresponding `bt2` index file suffixes.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash
@@ -789,6 +799,10 @@ If you want to use a pre-existing `picard CreateSequenceDictionary` dictionary
 file, use this to specify the required `.dict` file for the selected reference
 genome.
 
+> :warning: pre-built indices must currently be built on non-gzipped FASTA files
+> due to limitations of `samtools`. However once indices have been built, you
+> can re-gzip the FASTA file as nf-core will unzip this particular file for you.
+
 For example:
 
 ```bash
@@ -2382,7 +2396,7 @@ profiles {
     big_data {
       process {
         withName: markduplicates {
-          memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+          memory = 16.GB
         }
       }
     }
@@ -2393,6 +2407,12 @@ Where we have increased the default `4.GB` to `16.GB`. Make sure that you keep
 the `check_max` function, as this prevents your run asking for too much memory
 during retries.
 
+> Note that with this you will _not_ have the automatic retry mechanism. If
+> you want this, re-add the `check_max()` function on the `memory` line, and
+> add to the bottom of the entire file (outside the profiles block), the
+> block starting `def check_max(obj, type) {`, which is at the end of the
+> [nextflow.config file](https://github.com/nf-core/eager/blob/master/nextflow.config)
+
 Once saved, we can then modify your original Nextflow run command:
 
 ```bash

Dockerfile

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.2.0
+name: nf-core-eager-2.2.1
 channels:
   - conda-forge
   - bioconda

docs/images/usage/merging_files.png

@@ -348,6 +348,7 @@ if( params.bt2_index != '' && params.mapper == 'bowtie2' ){
         .into {bt2_index; bt2_index_bwamem}
 
     bwa_index = Channel.empty()
+    bwa_index_bwamem = Channel.empty()
 }
 
 // Validate BAM input isn't set to paired_end
@@ -855,6 +856,7 @@ if( params.bwa_index == '' && !params.fasta.isEmpty() && (params.mapper == 'bwaa
     mkdir BWAIndex && mv ${fasta}* BWAIndex
     """
     }
+    
     bt2_index = Channel.empty()
 }