Add docker build github action

[olgabot]

Many thanks to contributing to nf-core/kmermaid!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• PR is to dev rather than master
• 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 necessary, also make a PR on the nf-core/kmermaid branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/kmermaid/tree/master/.github/CONTRIBUTING.md

[pranathivemuri]

why is pysam and khmer removed?

[olgabot]

Khmer was there twice, once with 2.1.2 and another time with v 3.0.x and that was causing docker build issues

pysam dependency is handled by bam2fasta :)

[olgabot]

I know the tests are failing but this is because the khtools bloom-filter command is renamed to khtools index. I built the new image locally and the tests pass so I'm merging, because these tests are failing due to lack of samtools: #48

(base)
 Thu  9 Apr - 14:13  ~/code/nf-core/kmermaid--olgabot/docker-updates   olgabot/docker-updates ✔ 
  nextflow run -profile test_translate,docker .
N E X T F L O W  ~  version 20.01.0-rc1
Launching `./main.nf` [pensive_carlsson] - revision: 8df074499c
WARN: There's no process matching config selector: peptide_bloom_filter
WARN: There's no process matching config selector: extract_coding
[2m----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/kmermaid v1.0.0dev
----------------------------------------------------
Run Name          : pensive_carlsson
FASTAs            : https://github.com/nf-core/test-datasets/raw/kmermaid/reference/gencode.v32.pc_transcripts.subsample5.fa
K-mer sizes       : 3,9
Molecule          : dna,protein,dayhoff
Log2 Sketch Sizes : 2,4
One Sig per Record: true
Track Abundance   : false
Peptide fasta     : https://github.com/nf-core/test-datasets/raw/kmermaid/reference/gencode.v32.pc_translations.subsample5.randomseed0.fa
Peptide ksize     : 7
Peptide molecule  : protein
Bloom filter table size: 1e8
Max Resources     : 6 GB memory, 2 cpus, 2d time per job
Container         : docker - nfcore/kmermaid:dev
Output dir        : ./results
Launch dir        : /Users/olgabot/code/nf-core/kmermaid--olgabot/docker-updates
Working dir       : /Users/olgabot/code/nf-core/kmermaid--olgabot/docker-updates/work
Script dir        : /Users/olgabot/code/nf-core/kmermaid--olgabot/docker-updates
User              : olgabot
Config Profile    : test_translate,docker
Config Description: Minimal test dataset to check pipeline function
[0m----------------------------------------------------
executor >  local (27)
[7d/df0fbc] process > get_software_versions                    [100%] 1 of 1 ✔
[0c/3e99e8] process > make_protein_index                       [100%] 1 of 1 ✔
[22/f94c3a] process > translate                                [100%] 1 of 1 ✔
[31/4b80bd] process > sourmash_compute_sketch_fastx_nucleotide [100%] 4 of 4 ✔
[e0/cc9e72] process > sourmash_compute_sketch_fastx_peptide    [100%] 8 of 8 ✔
[4b/3fdf40] process > sourmash_compare_sketches                [100%] 12 of 12 ✔
[0;35mWarning, pipeline completed, but with errored process(es)
[0;31mNumber of ignored errored process(es) : 0
[0;32mNumber of successfully ran process(es) : 27
[0;35m[nf-core/kmermaid] Pipeline completed successfully

(base)
 Fri 10 Apr - 10:24  ~/code/nf-core/kmermaid--olgabot/docker-updates   olgabot/docker-updates ✔ 