Merge in Template V1.6.

[apeltzer]

Many thanks to contributing to nf-core/eager!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[jfy133]

I can't modify the files for some reason so sorry for all the comments.

[apeltzer]

No worries - just addressed all your mentioned issues. Troubleshooting is back, all other changes have been done and Maxime is on the authors list now 👍 Welcome @maxibor ;-)

[jfy133]

Good to go from my end

[apeltzer]

This just looks fancier than ever before:

INFO: ===========
 LINTING RESULTS
=================
 104 tests passed   0 tests had warnings   0 tests failed
The command "nf-core lint ${TRAVIS_BUILD_DIR}" exited with 0.
126.57s$ nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
N E X T F L O W  ~  version 0.32.0
Launching `/home/travis/build/nf-core/eager/main.nf` [boring_minsky] - revision: 1d1dd2b1ab
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/eager v2.0.7dev
----------------------------------------------------
Pipeline Name     : nf-core/eager
Pipeline Version  : 2.0.7dev
Run Name          : boring_minsky
Reads             : data/*{1,2}.fastq.gz
Fasta Ref         : https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta
BAM Index Type    : CSI
Data Type         : Paired-End
Skip Collapsing   : No
Skip Trimming     : No
Max Memory        : 6 GB
Max CPUs          : 2
Max Time          : 2d
Output dir        : ./results
Working dir       : /home/travis/build/nf-core/eager/tests/work
Container Engine  : docker
Container         : nfcore/eager:dev
Current home      : /home/travis
Current user      : travis
Current path      : /home/travis/build/nf-core/eager/tests
Script dir        : /home/travis/build/nf-core/eager
Config Profile    : test,docker
Config Description: Minimal test dataset to check pipeline function
----------------------------------------------------
[warm up] executor > local
[e3/5c2d3f] Submitted process > makeFastaIndex (Mammoth_MT_Krause.fasta)
[bb/c844bd] Submitted process > makeSeqDict (Mammoth_MT_Krause.fasta)
[5a/3591a9] Submitted process > makeBWAIndex (Mammoth_MT_Krause.fasta)
[63/29a32b] Submitted process > fastqc (JK2782_TGGCCGATCAACGA_L008)
[ae/239e99] Submitted process > fastqc (JK2785_TGGCCGATCAACGA_L008)
[c1/81d732] Submitted process > output_documentation (1)
[6d/5a9f1a] Submitted process > adapter_removal (JK2782_TGGCCGATCAACGA_L008)
[dd/bc54c9] Submitted process > adapter_removal (JK2785_TGGCCGATCAACGA_L008)
[44/f5ad86] Submitted process > fastqc_after_clipping (JK2782_TGGCCGATCAACGA_L008_R1_001)
[fb/090e0f] Submitted process > bwa (JK2782_TGGCCGATCAACGA_L008_R1_001)
[58/7c4390] Submitted process > bwa (JK2785_TGGCCGATCAACGA_L008_R1_001)
[ed/cc6ced] Submitted process > fastqc_after_clipping (JK2785_TGGCCGATCAACGA_L008_R1_001)
[83/fb42b7] Submitted process > samtools_idxstats (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted)
[3a/09d4a0] Submitted process > samtools_filter (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted.bam)
[44/50937a] Submitted process > damageprofiler (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted)
[05/fb2840] Submitted process > samtools_idxstats (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted)
[f9/737607] Submitted process > samtools_filter (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted.bam)
[f6/7da438] Submitted process > damageprofiler (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted)
[93/19c7ac] Submitted process > dedup (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[54/eb93e5] Submitted process > qualimap (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[94/d4b534] Submitted process > get_software_versions (1)
[53/8cd6be] Submitted process > get_software_versions (2)
[a9/ba65ba] Submitted process > dedup (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[7e/947a50] Submitted process > qualimap (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[bd/ed314b] Submitted process > preseq (JK2782_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[9a/adb2ca] Submitted process > preseq (JK2785_TGGCCGATCAACGA_L008_R1_001.sorted.bam.filtered)
[de/6f9511] Submitted process > multiqc
WARN: [nf-core/eager] Could not attach MultiQC report to summary email
Warning, pipeline completed, but with errored process(es) 
Number of ignored errored process(es) : 0 
Number of successfully ran process(es) : 27 
[nf-core/eager] Pipeline completed successfully
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
The command "nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference" exited with 0.