🎨 simplify input variables

[dmiller15]

Description

Effective change for users:

• The user is no longer required to provide the input type. The workflow will now attempt to autodetect whether the reads are paired or single end. If the user wishes to override the autodetection, they can provide the is_paired_end input
• The user is no longer required to provide kallisto_avg_frag_len and kallisto_std_dev for single end reads. The workflow will now attempt to autodetect the read length median and stddev values. If the user wishes to override the autodetection, they can provide the read_length_median and read_length_stddev values

Breakdown of changes:

• Removed input_type and paired inputs and replaced them with is_paired_end
• Added alignmentfile_pairedness script and tool to quickly ascertain whether an alignment file is paired end, single end, or mixed
• Modified the bam_strandness tool to output its determination of the whether the reads are paired or single end
• Replaced kallisto_avg_frag_len with read_length_median
• Replaced kallisto_std_dev with read_length_stddev
• Modified the bam_strandness tool to output what what it detects for read length median and stddev
• Used arriba_memory in arriba_draw as that step can have memory scaling needs

Closes https://github.com/d3b-center/bixu-tracker/issues/1871

Type of change

• [x] New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• [x] Single test: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/7e54a447-dc4d-424e-b251-83f4244773a5/#
• [x] Paired test: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/edbdc73b-9af5-4ebe-a691-18a0e8914661/#

Test Configuration:

• Environment:
• Test files:

Checklist:

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [x] I have committed any related changes to the PR

[dmiller15]

@migbro well running it in bash doesn't really change anything. I tried to throw pipefail in there but it failed because calling head on samtools view will actually result in a pipefail. The only way around that is to put in a || : (OR TRUE) thing. So overall pretty pointless here but it was nice to see it actually working.