Add step to filter gtf for only chromosomes that exist in the fasta file

[olgabot]

This keeps gffread from complaining, and allows one to use the new dev pipeline with iGenomes files that may have extra features in the GTF.

Address #272

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 necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repo PR: Add gtf line using chromosome not in genome test-datasets#68
• 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

[olgabot]

The -F flag in gffread adds all the GTF attributes to the fasta:

(sourmash-sbt2knn)
 Fri 30 Aug - 15:01  ~/ibm_lg/kmer-hashing/nextflow-intermediates/36/1916b1bf4672b99b68e879e8141dea 
  gffread -F -w transcripts.fa -g genome.fa genes_in_genome.gtf
(sourmash-sbt2knn)
 Fri 30 Aug - 15:03  ~/ibm_lg/kmer-hashing/nextflow-intermediates/36/1916b1bf4672b99b68e879e8141dea 
  gffread  -w transcripts_no_F.fa -g genome.fa genes_in_genome.gtf
head transcripts*
(sourmash-sbt2knn)
 Fri 30 Aug - 15:24  ~/ibm_lg/kmer-hashing/nextflow-intermediates/36/1916b1bf4672b99b68e879e8141dea 
  head transcripts*
==> transcripts.fa <==
>ENSPTRT00000074051 CDS=1-1158 gene_biotype=protein_coding gene_name=ENSPTRG00000041167 gene_source=ensembl gene_version=1 p_id=P6827 transcript_biotype=protein_coding transcript_source=ensembl transcript_version=1 tss_id=TSS28305 exon_version=1 protein_id=ENSPTRP00000060381 protein_version=1
ATGGCCTATTTAGGCCCATACCCTACGTCACTGCAGTCTCTGCAGATGAGGCTACTGCCTCACAACAGCC
TCCACAGGCACAGCTCCATCGTTACAATGGCCTCCTTAGACCCAGCTCCTGCCTCCCAGCCTTCTCTCCA
GGCCCTGAACTTTCTCAAGTCGACCTCACCAGGCCCAGTTCATGCTCCTTTGCAGCCTCTCCAGGCCCAG
CTCCTGCATCTTGGTGGCCCCTCCAGGCCCAGCCTCTGCCTCCCGTCGGCCTCTACAGTCCCAACATCTG
CCTCACAGCAGATTCTTCACGCCCAGCATCTGCCTCACTGTGGACCCCCCAAGCCAAGCTCCCAACCTTT
CAGCAGCTTCTACACACGCAGCTCCCACCTGCCAGTGGCCTCTTCAGGCCCATGGGGCTCATTCCTCACA
ACGGCCTTTCCAGGCCCAGTTTTTCCCTTCCGGCGTCCTCTCCGGGCCCAGAACCTCCTCAAGTCGGCCT
CTCCAGACCCACTTGCCCCCTCCGGGCGTCCTCTCTGGGCCCAGCTCTTCTTCCTGGTTGCGTCTCCAGG
CCCGACTCCTGCCTCTCAACAACCTCTTTGGACTCAGTGCCTACCCATCTCCTGGCGGCCTTGGTCGGCC

==> transcripts_no_F.fa <==
>ENSPTRT00000074051 CDS=1-1158
ATGGCCTATTTAGGCCCATACCCTACGTCACTGCAGTCTCTGCAGATGAGGCTACTGCCTCACAACAGCC
TCCACAGGCACAGCTCCATCGTTACAATGGCCTCCTTAGACCCAGCTCCTGCCTCCCAGCCTTCTCTCCA
GGCCCTGAACTTTCTCAAGTCGACCTCACCAGGCCCAGTTCATGCTCCTTTGCAGCCTCTCCAGGCCCAG
CTCCTGCATCTTGGTGGCCCCTCCAGGCCCAGCCTCTGCCTCCCGTCGGCCTCTACAGTCCCAACATCTG
CCTCACAGCAGATTCTTCACGCCCAGCATCTGCCTCACTGTGGACCCCCCAAGCCAAGCTCCCAACCTTT
CAGCAGCTTCTACACACGCAGCTCCCACCTGCCAGTGGCCTCTTCAGGCCCATGGGGCTCATTCCTCACA
ACGGCCTTTCCAGGCCCAGTTTTTCCCTTCCGGCGTCCTCTCCGGGCCCAGAACCTCCTCAAGTCGGCCT
CTCCAGACCCACTTGCCCCCTCCGGGCGTCCTCTCTGGGCCCAGCTCTTCTTCCTGGTTGCGTCTCCAGG
CCCGACTCCTGCCTCTCAACAACCTCTTTGGACTCAGTGCCTACCCATCTCCTGGCGGCCTTGGTCGGCC

[apeltzer]

Retriggered the tests after merging in the GFF one - we'll see soon if things work fine 👍

[apeltzer]

Some questions / points :-)

[olgabot]

Yay passing finally!

[apeltzer]

Still something broken 👎

[olgabot]

Aaah sorry about that. Will fix.

[olgabot]

Okay ready when you are!

[apeltzer]

Looking good to me 👍