OK I need some nf-test/nft-utils experts: https://github.com/nf-core/taxprofiler/pull/695 Why is my

.nftignore

file being... ignored 😕 the snapshot is picking up md5sums for fastqc/and bbduk log files although they are excluded in the ignore file 😞

I am looking at it

Thank you, also realised it was sort of unfair to ask you privately so I opned it a bit wider 😉

Let me try something locally

I'm confused because it works with or other test profile

IT TAKES forever to run

maaaybe

I think I got it

Please enlighten me oh oracle, this has been bugging me for days

be prepared

oh no

basically you have the expected results, because the path is wrong

yes

Ahhhh

hence you don't need it in the .nftignore

So it's trying to ignore e.g.

outDir/fastqc/fastqc/*zip

?

this is the list of fastqc files from stable_name_all: "fastqc", "fastqc/processed", "fastqc/processed/2612_ERR5766176_B_processed_1_fastqc.html", "fastqc/processed/2612_ERR5766176_B_processed_1_fastqc.zip", "fastqc/processed/2612_ERR5766176_B_processed_2_fastqc.html", "fastqc/processed/2612_ERR5766176_B_processed_2_fastqc.zip", "fastqc/processed/2612_ERR5766176_processed_1_fastqc.html", "fastqc/processed/2612_ERR5766176_processed_1_fastqc.zip", "fastqc/processed/2612_ERR5766176_processed_2_fastqc.html", "fastqc/processed/2612_ERR5766176_processed_2_fastqc.zip", "fastqc/processed/2613_ERR5766181_processed_1_fastqc.html", "fastqc/processed/2613_ERR5766181_processed_1_fastqc.zip", "fastqc/processed/2613_ERR5766181_processed_2_fastqc.html", "fastqc/processed/2613_ERR5766181_processed_2_fastqc.zip", "fastqc/processed/ERR3201952_ERR3201952_processed_fastqc.html", "fastqc/processed/ERR3201952_ERR3201952_processed_fastqc.zip", "fastqc/raw", "fastqc/raw/2612_ERR5766176_B_raw_1_fastqc.html", "fastqc/raw/2612_ERR5766176_B_raw_1_fastqc.zip", "fastqc/raw/2612_ERR5766176_B_raw_2_fastqc.html", "fastqc/raw/2612_ERR5766176_B_raw_2_fastqc.zip", "fastqc/raw/2612_ERR5766176_raw_1_fastqc.html", "fastqc/raw/2612_ERR5766176_raw_1_fastqc.zip", "fastqc/raw/2612_ERR5766176_raw_2_fastqc.html", "fastqc/raw/2612_ERR5766176_raw_2_fastqc.zip", "fastqc/raw/2613_ERR5766181_raw_1_fastqc.html", "fastqc/raw/2613_ERR5766181_raw_1_fastqc.zip", "fastqc/raw/2613_ERR5766181_raw_2_fastqc.html", "fastqc/raw/2613_ERR5766181_raw_2_fastqc.zip", "fastqc/raw/ERR3201952_ERR3201952_raw_fastqc.html", "fastqc/raw/ERR3201952_ERR3201952_raw_fastqc.zip",

you want all files from outputDir/fastqc

Wait what do yo um ean by this

list of fastqc files: def stable_name_fastqc = getAllFilesFromDir("$outputDir/fastqc", relative: true, includeDir: true, ignoreFile: 'tests/.nftignore') "processed", "processed/2612_ERR5766176_B_processed_1_fastqc.html", "processed/2612_ERR5766176_B_processed_1_fastqc.zip", "processed/2612_ERR5766176_B_processed_2_fastqc.html", "processed/2612_ERR5766176_B_processed_2_fastqc.zip", "processed/2612_ERR5766176_processed_1_fastqc.html", "processed/2612_ERR5766176_processed_1_fastqc.zip", "processed/2612_ERR5766176_processed_2_fastqc.html", "processed/2612_ERR5766176_processed_2_fastqc.zip", "processed/2613_ERR5766181_processed_1_fastqc.html", "processed/2613_ERR5766181_processed_1_fastqc.zip", "processed/2613_ERR5766181_processed_2_fastqc.html", "processed/2613_ERR5766181_processed_2_fastqc.zip", "processed/ERR3201952_ERR3201952_processed_fastqc.html", "processed/ERR3201952_ERR3201952_processed_fastqc.zip", "raw", "raw/2612_ERR5766176_B_raw_1_fastqc.html", "raw/2612_ERR5766176_B_raw_1_fastqc.zip", "raw/2612_ERR5766176_B_raw_2_fastqc.html", "raw/2612_ERR5766176_B_raw_2_fastqc.zip", "raw/2612_ERR5766176_raw_1_fastqc.html", "raw/2612_ERR5766176_raw_1_fastqc.zip", "raw/2612_ERR5766176_raw_2_fastqc.html", "raw/2612_ERR5766176_raw_2_fastqc.zip", "raw/2613_ERR5766181_raw_1_fastqc.html", "raw/2613_ERR5766181_raw_1_fastqc.zip", "raw/2613_ERR5766181_raw_2_fastqc.html", "raw/2613_ERR5766181_raw_2_fastqc.zip", "raw/ERR3201952_ERR3201952_raw_fastqc.html", "raw/ERR3201952_ERR3201952_raw_fastqc.zip"

I want to exclude

you want all files from outputDir/fastqc/*/*.{zip,html}

becuase they are variableyou want all files from outputDir/fastqc

I think it's because of getAllFilesFromDir("$outputDir/fastqc",

OK

Let me propose another idea that should be good for your setup

But it's making me again not like the

.nftiognore

😆

she does not try to snapshot content of fastqc files

No, but she does it for others I think... ah but maybe doesn't need to mix with ignore...

Maxime is right, I do not try to do snapshot of fastqc files.

I propose this:

def stable_name_all               = getAllFilesFromDir(params.outdir, relative: true,  includeDir: true,  ignore: ['pipeline_info/*.{html,json,txt}'])
            def stable_content_adapterremoval = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["adapterremoval/*"])
            def stable_content_bbduk          = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["bbduk/*"])
            def stable_content_fastqc         = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["fastqc/*"])
            def stable_content_filtlong       = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["filtlong/*"])
            def stable_content_bowtie2        = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["bowtie2/*"])
            def stable_content_kaiju          = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["kaiju/*"])
            def stable_content_kraken2        = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["kraken2/*"])
            def stable_content_porechop       = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["porechop/*"])
            def stable_content_samtools       = getAllFilesFromDir(params.outdir, relative: false, includeDir: false, ignoreFile: 'tests/.nftignore', include: ["samtools/*"])

Haven't had a chance to try it yet but I'm very excited to try it

good point

Ugh one more variable file

you could add this to the docs in https://github.com/nf-core/nft-utils

Where though... the structure is a bit difficult to shoe horn it in (I was looking there previously)(