Template merge

[lekhakaranam]

Many thanks to contributing to nf-core/kmermaid!

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• PR is to dev rather than master
• This comment contains a description of changes (with reason)
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[olgabot]

@lekhakaranam I'm also getting docker build and other errors, seemingly because of sourmash/bam2fasta/pysam/samtools conflicts. @pranathivemuri can you offer any insight?

(base)
 Fri  7 Aug - 08:04  ~/code/nf-core/kmermaid--olgabot/lekha-template   template_merge ✔ 
  docker build -t nfcore/kmermaid:template .
Sending build context to Docker daemon  11.34MB
Step 1/11 : FROM nfcore/base:1.9
 ---> f1c63ec29383
Step 2/11 : LABEL authors="Olga Botvinnik"       description="Docker image containing all software requirements for the nf-core/kmermaid pipeline"
 ---> Using cache
 ---> 40bc4d13ad0d
Step 3/11 : COPY environment.yml /
 ---> 7e4421061611
Step 4/11 : RUN conda env create -f /environment.yml && conda clean -a
 ---> Running in 948333058ad7
Collecting package metadata (repodata.json): ...working... done

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package libdeflate conflicts for:
bioconda::sourmash=3.2.2 -> bam2fasta[version='>=1.0.1'] -> pysam -> libdeflate[version='>=1.0,<1.1.0a0|>=1.3,<1.4.0a0|>=1.5,<1.6.0a0|>=1.6,<1.7.0a0']
pysam=0.15.4 -> libdeflate[version='>=1.5,<1.6.0a0']
bioconda::samtools=1.10 -> htslib[version='>=1.10,<1.11.0a0'] -> libdeflate[version='>=1.3,<1.4.0a0|>=1.6,<1.7.0a0']

The command '/bin/sh -c conda env create -f /environment.yml && conda clean -a' returned a non-zero code: 1

[olgabot]

Okay I changed sourmash to use sourmash-minimal from conda-forge instead since we're just using the basic features and isolated the problem to just pysam and samtools:

(base)
 ✘  Fri  7 Aug - 08:21  ~/code/nf-core/kmermaid--olgabot/lekha-template   template_merge ✔ 
  docker build -t nfcore/kmermaid:dev .
Sending build context to Docker daemon  11.36MB
Step 1/11 : FROM nfcore/base:1.9
 ---> f1c63ec29383
Step 2/11 : LABEL authors="Olga Botvinnik"       description="Docker image containing all software requirements for the nf-core/kmermaid pipeline"
 ---> Using cache
 ---> 40bc4d13ad0d
Step 3/11 : COPY environment.yml /
 ---> fce08e89220d
Step 4/11 : RUN conda env create -f /environment.yml && conda clean -a
 ---> Running in 3cbd60425d4f
Collecting package metadata (repodata.json): ...working... done

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package libdeflate conflicts for:
pysam=0.15.4 -> libdeflate[version='>=1.5,<1.6.0a0']
bioconda::samtools=1.10 -> htslib[version='>=1.10,<1.11.0a0'] -> libdeflate[version='>=1.3,<1.4.0a0|>=1.6,<1.7.0a0']

[olgabot]

We're already at the latest version of samtools, bioconda::samtools=1.10 but right now I'm testing upgrading pysam=0.15.4 --> bioconda::pysam=0.16.0 and it seems to be at least building! We'll see if the tests pass :)

[pranathivemuri]

what are igenomes for?

[pranathivemuri]

@olgabot now the tests are actually failing, let me know if you would like to look at it together tomorrow - get_software_versions is failing but there is no exact way to find out which of the packages is missing, would like your input - I fixed the linting issues, missing schema.json, Dockerfile formatting

so after this PR - #30 there was no automatic TEMPLATE branch setup as per the instructions here - https://nf-co.re/developers/sync#setting-up-a-pipeline-for-syncing-retrospectively
which is forcing us to manually sync now. please correct me if I am wrong!

We have to definitely do it this time so we don't suffer through this again

[olgabot]

I think I see what's happening:

WARN: Access to undefined parameter `publish_dir_mode` -- Initialise it to a default value eg. `params.publish_dir_mode = some_value`
Error executing process > 'sourmash_compute_sketch_fastx_nucleotide (SRR4050380__molecule-dna__ksize-3__num_hashes-4__track_abundance-false)'

Caused by:
  No enum constant nextflow.processor.PublishDir.Mode.NULL

From: https://github.com/nf-core/kmermaid/pull/93/checks?check_run_id=1192829083

[olgabot]

Suggested change

- conda-forge::sourmash-minimal=3.5.0