Improve pipeline tests

[apeltzer]

This adds testing for more than one sample to the pipeline.

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 .).
• CHANGELOG.md is updated

[jfy133]

When testing the add_more_tests branch from apeltzer/eager, I get an error at indexing the reference genome.

command:

nextflow run apeltzer/eager \ 
-profile shh \
--reads '/projects1/users/fellows/nextflow/eager2/dev_testing/data/{ABM006.A0101,DJA002.A0101}/*_R{1,2}*fastq.gz' \ 
--pairedEnd \
--fasta '/projects1/users/fellows/nextflow/eager2/dev_testing/references/tannerella_forsythia_actual/Tannerella_forsythia_9212.fa' \
--outdir '/projects1/users/fellows/nextflow/eager2/dev_testing/eager2/01-actual_reference/tannerella_forsythia/Multiple' \
--name 'eager_nextflow_dev' \
--email fellows@shh.mpg.de \
--max_cpus 3 \
--max_mem 32G \
--skip_preseq \
--min_adap_overlap 1 \
--clip_readlength 30 \
--clip_min_read_quality 20 \ 
--bwaalnn 0.01 \ 
--bwalnl 32 \ 
--bam_discard_unmapped \ 
--bam_unmapped_type discard \ 
--dedupper dedup \ 
--dedup_all_merged \ 
-r add_more_tests 

Error:

Jan-21 20:34:30.410 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 767025; id: 2; name: makeFastaIndex (Tannerella_forsythia_9212.fa); status: COMPLETED; exit: 127; error: -; workDir: /projects1/users/fellows/nextflow/eager2/dev_testing/eager2/01-actual_reference/tannerella_forsythia/Multiple/work/e6/c5367be18c011a15d361bd1fa4631d started: 1548099270404; exited: 2019-01-21T19:34:26Z; ]
Jan-21 20:34:30.450 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'makeFastaIndex (Tannerella_forsythia_9212.fa)' 

Caused by:
  Process `makeFastaIndex (Tannerella_forsythia_9212.fa)` terminated with an error exit status (127) 

Command executed:
 
  samtools faidx Tannerella_forsythia_9212.fa

Command exit status: 
  127

Command output: 
  (empty)

Command error: 
  /bin/bash: line 0: cd: /projects1/users/fellows/nextflow/eager2/dev_testing/eager2/01-actual_reference/tannerella_forsythia/Multiple/work/e6/c5367be18c011a15d361bd1fa4631d: No such file or directory
  /bin/bash: .command.stub: No such file or directory
 
Work dir:
  /projects1/users/fellows/nextflow/eager2/dev_testing/eager2/01-actual_reference/tannerella_forsythia/Multiple/work/e6/c5367be18c011a15d361bd1fa4631d

Same command with nf-core/eager version 2.0.4 worked previously.

Will send link to output directory on slack

[apeltzer]

Looks like a weird Singularity problem again. It's not complaining about pipeline code, but about missing dependencies etc....