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Add nf-test #1063

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f7fceaf
Add general structure, and generate (not working!) snapshot for basic…
jfy133 Apr 26, 2024
0778e58
Try adding an ignore zip system, doesn't work atm though...
jfy133 Apr 26, 2024
eb73ae6
Merge branch 'dev' into nf-test-conversionMerge in from dev
jfy133 Jun 28, 2024
cc114f3
Continue customisation
jfy133 Jun 28, 2024
37994df
More debugging
jfy133 Jul 12, 2024
e07dc06
Get working function
jfy133 Jul 19, 2024
c0f93d9
Get working function properly, and start integrating into snapshot: p…
jfy133 Jul 19, 2024
de035ca
Extract names properly
jfy133 Jul 19, 2024
7890575
Remove unnecesary code
jfy133 Jul 19, 2024
b795b9e
Get working string check function!
jfy133 Jul 19, 2024
cac8152
TODO
jfy133 Jul 19, 2024
a8dcd64
Update MQC so works on gitpod, try to re-add original getAllFilesFrom…
jfy133 Jul 20, 2024
56cba0c
And get it back again
jfy133 Jul 20, 2024
0f12b21
Sort output to ensure consistency
jfy133 Jul 22, 2024
d41aad9
Sort file name only funciton
jfy133 Jul 22, 2024
61c4d24
Start testing preprocessing
jfy133 Jul 26, 2024
19db88c
Merge branch 'dev' into nf-test-conversion
jfy133 Jul 26, 2024
bcc3baf
Start adding preprocessing dir but diff not working so can't ser vari…
jfy133 Jul 26, 2024
0b58cf7
Backing up TODO notes
jfy133 Jul 26, 2024
eb4824e
Final snapshots, need to double check all files are covered but I thi…
jfy133 Aug 16, 2024
9ce930f
Finalise first test
jfy133 Sep 20, 2024
5598eec
Merge branch 'dev' into nf-test-conversion
jfy133 Sep 20, 2024
6362fa3
Update tests to latest dev
jfy133 Sep 20, 2024
61086b5
Merge branch 'dev' into nf-test-conversion
jfy133 Oct 4, 2024
9a56d48
Merge branch 'dev' into nf-test-conversion
jfy133 Oct 4, 2024
bb12ca1
Start refactoring to use nft-utils
jfy133 Oct 4, 2024
87fafc5
fix qualimap output dir typo
TCLamnidis Oct 11, 2024
ef71d3b
no sampleid in qualimap outdir
TCLamnidis Oct 11, 2024
a7fadc6
bump nft-utils version
TCLamnidis Oct 18, 2024
4baefaf
start refactoring to use nft-utils
TCLamnidis Oct 18, 2024
8b7e950
update snapshot. Not sure it works yet.
TCLamnidis Oct 18, 2024
2e5bf4f
add preprocessing
TCLamnidis Nov 8, 2024
c204fe9
fix preprocessing checks
TCLamnidis Nov 29, 2024
4efc86b
Merge remote-tracking branch 'origin/dev' into nf-test-conversion
TCLamnidis Nov 30, 2024
9f3611f
Merge remote-tracking branch 'origin/dev' into nf-test-conversion
TCLamnidis Dec 3, 2024
6893eb6
reorder and add todos
TCLamnidis Dec 3, 2024
13a640c
remove versions.ymls from snapshot
TCLamnidis Dec 3, 2024
5241ffc
check bam names instead of content
TCLamnidis Dec 4, 2024
0dab178
add ave_filtered_bam parameter to test profile
TCLamnidis Dec 4, 2024
01850ad
fix result pickup for bam filtering and deduplication
TCLamnidis Dec 4, 2024
42b3a47
add final_bams,mapstats. fix mapping. remove old code
TCLamnidis Dec 6, 2024
0c6c8e3
simplify bam_input_stats snapshot
TCLamnidis Dec 6, 2024
50ea5e1
update snapshot
TCLamnidis Dec 6, 2024
997fb5b
exclude unstable qualimap results.
TCLamnidis Dec 6, 2024
82cb639
Check existence of Multiqc output files. reorder tests to match alpha…
TCLamnidis Dec 11, 2024
61f6285
Merge branch 'dev' into nf-test-conversion
TCLamnidis Dec 15, 2024
c0cd1eb
remove leftover todo
TCLamnidis Dec 20, 2024
53d82b0
Merge branch 'nf-test-conversion' of github.com:nf-core/eager into nf…
TCLamnidis Dec 20, 2024
5ed2b0b
add command legend, and align a bit more
TCLamnidis Dec 20, 2024
80007d7
Fix test. and snapshot.
TCLamnidis Jan 24, 2025
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Backing up TODO notes
jfy133 committed Jul 26, 2024
commit 0b58cf7d57aa3f94128856948aa95c8002498217
3 changes: 2 additions & 1 deletion tests/test.nf.test
Original file line number Diff line number Diff line change
@@ -35,7 +35,8 @@ nextflow_pipeline {

// Preprcoessing

{ assert snapshot( path("$outputDir/preprocessing/") ).match("processing_fastp") }, // TODO: check all three stable (I suspect log/html might not be)
{ assert snapshot( path("$outputDir/preprocessing/fastp") ).match("processing_fastp") }, // TODO: Stable: JSON, varaible: HTML, LOG
{ assert snapshot( path("$outputDir/preprocessing/fastp") ).match("processing_fastp") }, // TODO: Stable: HTML, variable: ZIP
//{ assert snapshot( path("$outputDir/preprocessing/fastqc_raw").list().findAll{ it.toString() }).match("processing_fastqc_raw") },
//{ assert snapshot( path("$outputDir/preprocessing/fastqc_preprocessed").list().findAll{ it.toString() }).match("processing_fastqc_preprocessed") },
//{ assert snapshot( path("$outputDir/final_bams") ).match("final_bams") },