nf-core_modules/tests/software/last/lastal/test.yml
Charles Plessy 207930139a
New last/lastal module to align query sequences on a target index (#510)
* New last/lastal to align query sequences on a target index

`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite.  It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences.  The index is produced by
the `lastdb` program (module `last/lastdb`).  The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`).  For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.

The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Un-hardcode the path to the LAST index.

Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder.  Not failing would
result in feeding garbage information in the INDEX_NAME variable.

    basename \$(ls $index/*.bck) .bck

In case of missing file, a clear error message is given by `ls`.  In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately.  (`basename: extra operand ‘.bck’`)

Alternatives that do not fail if there is no .bck file:

    basename $index/*bck .bck
    find $index -name '*bck' | sed 's/.bck//'

Alternatives that do not fail if there are more than one .bck file:

    basename -s .bck $index/*bck
    ls $index/*.bck | xargs basename -s .bck
    find $index -name '*bck' | sed 's/.bck//'

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:10:48 +01:00

45 lines
1.9 KiB
YAML

- name: last lastal test_last_lastal_with_dummy_param_file
command: nextflow run tests/software/last/lastal -entry test_last_lastal_with_dummy_param_file -c tests/config/nextflow.config
tags:
- last
- last/lastal
files:
- path: output/last/contigs.genome.maf.gz
md5sum: 33e9098d8242b0aac829339c03fe94aa
- path: output/untar/lastdb/genome.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/untar/lastdb/genome.des
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/untar/lastdb/genome.prj
md5sum: 489715f14b0fea6273822696e72357f9
- path: output/untar/lastdb/genome.sds
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
- path: output/untar/lastdb/genome.ssp
md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
- path: output/untar/lastdb/genome.suf
md5sum: 1895efa8653e8e9bd3605cff0408ed33
- path: output/untar/lastdb/genome.tis
md5sum: b7c40f06b1309dc6f37849eeb86dfd22
- name: last lastal test_last_lastal_with_real_param_file
command: nextflow run tests/software/last/lastal -entry test_last_lastal_with_real_param_file -c tests/config/nextflow.config
tags:
- last
- last/lastal
files:
- path: output/last/contigs.genome.maf.gz
md5sum: 3a0f42e76da9549748983ac4d7ff7473
- path: output/untar/lastdb/genome.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/untar/lastdb/genome.des
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/untar/lastdb/genome.prj
md5sum: 489715f14b0fea6273822696e72357f9
- path: output/untar/lastdb/genome.sds
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
- path: output/untar/lastdb/genome.ssp
md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
- path: output/untar/lastdb/genome.suf
md5sum: 1895efa8653e8e9bd3605cff0408ed33
- path: output/untar/lastdb/genome.tis
md5sum: b7c40f06b1309dc6f37849eeb86dfd22