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fix input schema to accept uncompressed fasta; fix #309 #310

Merged
merged 3 commits into from
Oct 13, 2023
Merged

fix input schema to accept uncompressed fasta; fix #309 #310

merged 3 commits into from
Oct 13, 2023

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tavareshugo
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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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

This should fix #309 that errors when uncompressed files are given as input.
I also added support for fas extension.

I have tested the workflow using all uncompressed and compressed formats as input.

Click here for code used to generate the test data. 
mkdir -p data

# download test data
# wget didn't actually work, downloaded it manually
wget -O data/s1.fasta.gz "https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/wastewater_metagenome_contigs_1.fasta.gz"
wget -O data/s2.fasta.gz "https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/wastewater_metagenome_contigs_2.fasta.gz"

# make uncompressed copies with different extensions
# and populate a samplesheet
echo "sample,fasta" > samplesheet.csv
for i in s1 s2
do
  # add the original fasta to samplesheet
  echo "${i}_fasta,data/$i.fasta" >> samplesheet.csv
  echo "${i}_fasta.gz,data/$i.fasta.gz" >> samplesheet.csv

  # uncompressed version
  gzcat data/$i.fasta.gz > data/$i.fasta

  # copies of each extension
  for j in fas fa fna
  do
    cp data/$i.fasta.gz data/$i.$j.gz
    cp data/$i.fasta data/$i.$j

    # populate the samplesheet
    echo "$i,data/$i.$j" >> samplesheet.csv
    echo "$i,data/$i.$j.gz" >> samplesheet.csv
  done
done

The code above generates the files and respective samplesheet:

sample,fasta
s1_fasta,data/s1.fasta
s1_fasta_gz,data/s1.fasta.gz
s1_fas,data/s1.fas
s1_fas_gz,data/s1.fas.gz
s1_fa,data/s1.fa
s1_fa_gz,data/s1.fa.gz
s1_fna,data/s1.fna
s1_fna_gz,data/s1.fna.gz
s2_fasta,data/s2.fasta
s2_fasta_gz,data/s2.fasta.gz
s2_fas,data/s2.fas
s2_fas_gz,data/s2.fas.gz
s2_fa,data/s2.fa
s2_fa_gz,data/s2.fa.gz
s2_fna,data/s2.fna
s2_fna_gz,data/s2.fna.gz

I then ran the test as follows (funcscan/main.nf points to my local clone):

nextflow funcscan/main.nf -profile test,singularity --input samplesheet.csv --outdir results

This mixed bag of formats all worked successfully:

executor >  local (398)
[a6/b62a61] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_FASTA_PREP (s1.fas.gz)                      [100%] 8 of 8 ✔
[f5/6d0393] process > NFCORE_FUNCSCAN:FUNCSCAN:BIOAWK (s1_fas_gz)                                 [100%] 16 of 16 ✔
[c0/b6267f] process > NFCORE_FUNCSCAN:FUNCSCAN:PRODIGAL_GFF (s1_fas_gz)                           [100%] 16 of 16 ✔
[e3/ef2c17] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_PRODIGAL_FAA (s1_fas_gz.faa.gz)             [100%] 16 of 16 ✔
[dc/d89187] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_PRODIGAL_FNA (s1_fas_gz.fna.gz)             [100%] 16 of 16 ✔
[0b/f4f7bb] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_PRODIGAL_GFF (s1_fas_gz.gff.gz)             [100%] 16 of 16 ✔
[25/d14230] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPLIFY_PREDICT (s1_fas_gz)                    [100%] 16 of 16 ✔
[9d/ec2e9e] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS (s1_fas_gz)                     [100%] 16 of 16 ✔
[a0/2d3305] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED (s1_fas_gz.prediction.gz)   [100%] 16 of 16 ✔
[0c/849cee] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS (s1_fas_gz.all_orfs.faa.gz) [100%] 16 of 16 ✔
[65/1c840a] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR (s1_fas_gz)                              [100%] 16 of 16 ✔
[ea/cc2c44] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMP_HMMER_HMMSEARCH (s1_fas_gz)                [100%] 16 of 16 ✔
[63/441d8b] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD                                 [100%] 1 of 1 ✔
[5c/a49d25] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI (s2_fa)                               [100%] 16 of 16 ✔
[55/88d7ab] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:TABIX_BGZIP (ampcombi_complete_summary)        [100%] 1 of 1 ✔
[9c/a2b5b4] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_UPDATE (update)                  [100%] 1 of 1 ✔
[19/91212b] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN (s2_fa_gz)                   [100%] 16 of 16 ✔
[83/930e8d] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_AMRFINDERPLUS (s2_fa_gz)         [100%] 16 of 16 ✔
[88/bea5f5] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:FARGENE (s1_fas_gz)                            [100%] 32 of 32 ✔
[7a/a5fbb7] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_FARGENE (s1_fas_gz)              [100%] 64 of 64 ✔
[19/96f68b] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:RGI_MAIN (s1_fas_gz)                           [100%] 16 of 16 ✔
[b1/a05766] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_RGI (s1_fas_gz)                  [100%] 16 of 16 ✔
[86/552db3] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:ABRICATE_RUN (s1_fas_gz)                       [100%] 16 of 16 ✔
[f4/a887b2] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_ABRICATE (s1_fas_gz)             [100%] 16 of 16 ✔
[ff/28d892] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_SUMMARIZE                        [100%] 1 of 1 ✔
[f2/436bc1] process > NFCORE_FUNCSCAN:FUNCSCAN:CUSTOM_DUMPSOFTWAREVERSIONS (1)                    [100%] 1 of 1 ✔
[71/dd9844] process > NFCORE_FUNCSCAN:FUNCSCAN:MULTIQC                                            [100%] 1 of 1 ✔
-[nf-core/funcscan] Pipeline completed successfully-
Completed at: 15-Sep-2023 18:16:43
Duration    : 1h 6m 47s
CPU hours   : 2.9
Succeeded   : 398

Version:

N E X T F L O W
version 23.04.1 build 5866
created 15-04-2023 06:51 UTC (07:51 BST)
cite doi:10.1038/nbt.3820
http://nextflow.io

@jfy133
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jfy133 commented Sep 21, 2023

@nf-core/funcscan can someone test this please?

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github-actions bot commented Sep 21, 2023 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bd61a80

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-11 11:45:37

@jasmezz jasmezz self-requested a review September 27, 2023 08:45
@jasmezz
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jasmezz commented Sep 29, 2023

@tavareshugo Can you pull dev to your fork and into this branch? This should resolve the CI check errors.

@tavareshugo
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@jasmezz ,apologies, I realise now that I should have worked from dev to start with. I have merged your dev branch to my fork. I hope this works.

@jfy133
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jfy133 commented Oct 11, 2023

Ignore nf-core linting for now

@jasmezz
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jasmezz commented Oct 11, 2023

I am running the non-bakta CI checks manually now to have at least the prokka/prodigal BGC workflows succeeding.

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jasmezz commented Oct 11, 2023

More checks failing due to no-space-left-on-device. I'd go ahead since we cannot change that.

@jfy133
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jfy133 commented Oct 12, 2023

Before merging, one mlast thing: @tavareshugo can you update the changelog and tag yoursself in it :)

@jasmezz
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jasmezz commented Oct 13, 2023

@tavareshugo You can use this text line for the update, if you want.

@tavareshugo
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Thanks both. Done!

@jasmezz jasmezz merged commit ffba284 into nf-core:dev Oct 13, 2023
@tavareshugo tavareshugo deleted the fix_gz branch October 13, 2023 10:49
@jasmezz jasmezz mentioned this pull request Oct 13, 2023
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@tavareshugo @jfy133 @jasmezz