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Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. #5278

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merged 2 commits into from
Mar 19, 2024
Merged

Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. #5278

merged 2 commits into from
Mar 19, 2024

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@adamrtalbot adamrtalbot commented Mar 19, 2024 •
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The FASTQ_FASTQC_UMITOOLS_FASTP subworkflow included an absolute path in the snapshot because it was passing the input file to the output channel directly without modification for the parameter skip_trimming when no UMI processing was occurring.

This PR reduces the stringency of this specific test slightly to work around this issue.

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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@adamrtalbot adamrtalbot mentioned this pull request Mar 19, 2024
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pinin4fjords
pinin4fjords approved these changes Mar 19, 2024
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LGTM

@adamrtalbot adamrtalbot added this pull request to the merge queue Mar 19, 2024
@adamrtalbot adamrtalbot mentioned this pull request Mar 19, 2024
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Merged via the queue into nf-core:master with commit cabcc0d Mar 19, 2024
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@adamrtalbot adamrtalbot deleted the fastq_fastqc_umitools_fastp_fixed_test branch March 19, 2024 17:06
jvfe added a commit to jvfe/modules that referenced this pull request Mar 19, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
e16f6f9 
* master:
  Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute path in the snapshot. (nf-core#5278)
  added new module lofraq/viterbi; solves new module: lofreq/viterbi nf-core#5158 (nf-core#5197)
  Update glimpse/phase output channel to phased_variants nf-core#5172 (nf-core#5174)
  Add module: GTFSORT (nf-core#5237)
  add nf-test to bedtools/sort - nf-core#3936 (nf-core#5221)
  addedd optional output channel for lib files (nf-core#5257)
vlebars pushed a commit to vlebars/modules that referenced this pull request Mar 20, 2024
@adamrtalbot
Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute p…
fd36f06 
…ath in the snapshot. (nf-core#5278)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@adamrtalbot @tucano
Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute p…
fc86c95 
…ath in the snapshot. (nf-core#5278)
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@adamrtalbot @jennylsmith
Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute p…
05810c9 
…ath in the snapshot. (nf-core#5278)
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@adamrtalbot
Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute p…
6058576 
…ath in the snapshot. (nf-core#5278)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 22, 2024
@adamrtalbot @tucano
Fix test for FASTQ_FASTQC_UMITOOLS_FASTP which included an absolute p…
9b5d858 
…ath in the snapshot. (nf-core#5278)
@adamrtalbot adamrtalbot mentioned this pull request Jun 20, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@robsyme robsyme Awaiting requested review from robsyme

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