12 commits

Author	SHA1	Message	Date
Harshil Patel	65a3422686	Add default publish_dir for index processes (#428)	2021-04-10 20:49:09 +01:00
Harshil Patel	dce27b8102	Update functions.nf to be more flexible for publishing by meta keys (#423) ... * Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint	2021-04-09 17:23:56 +01:00
Jose Espinosa-Carrasco	ee90e7af77	Add default output dir for modules that create indices, updated (#336) ... * Add default output dir for modules that create indices * Change path for index module test output * Fix bowtie2/align tests * Fixing bowtie/align tests * Fix genomegenerate test * Fixing README linting	2021-03-23 17:55:01 +00:00
Jose Espinosa-Carrasco	572abb00b3	Remove def from module options definition in main (#270) ... * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo	2021-03-15 12:16:43 +00:00
drpatelh	dcc580e4fb	Remove Conda build ids for all modules	2021-02-16 23:58:23 +00:00
drpatelh	3ae4c51f42	various - add build to conda definition	2021-02-03 09:20:34 +00:00
Edmund Miller	d76638d6f8	style(#77): Fix editorconfig errors	2020-12-17 17:50:24 -06:00
drpatelh	047dbde0af	Add singularity containers for rnaseq pipeline modules	2020-12-13 23:41:53 +00:00
drpatelh	42f318fe75	Update Salmon modules	2020-12-09 21:20:11 +00:00
drpatelh	a3f46865ff	Remove Singularity image path	2020-11-12 14:55:16 +00:00
drpatelh	14525ed50d	Remove functions file	2020-10-14 18:29:50 +01:00
drpatelh	cbf8329ffd	Add new modules	2020-09-10 16:09:54 +01:00