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Refactoring #172

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merged 133 commits into from
Feb 28, 2024
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ff0c46a
size reduction
erinyoung Jan 24, 2024
a405ede
moving to nf-core compatible
erinyoung Jan 26, 2024
a1fb5e8
sample to prefix
erinyoung Jan 27, 2024
ab20500
adding fastas
erinyoung Jan 27, 2024
c730624
update kraken2 and mash ref
erinyoung Jan 29, 2024
e670381
added version
erinyoung Jan 29, 2024
7450ad8
initial script for multiqc versions
erinyoung Jan 29, 2024
6b982b7
updated tag
erinyoung Jan 29, 2024
9a352df
updated tag
erinyoung Jan 29, 2024
ae39200
updated tag
erinyoung Jan 29, 2024
5d0f563
added versions
erinyoung Jan 29, 2024
541f8f0
added versions
erinyoung Jan 30, 2024
b6f335c
added versions
erinyoung Jan 30, 2024
468cfc7
read in fastas from path
erinyoung Jan 30, 2024
c2d90a3
change module path
erinyoung Jan 30, 2024
55cf6eb
change module path
erinyoung Jan 30, 2024
0b65ccb
moving to panaroo
erinyoung Jan 30, 2024
c71da15
change module path
erinyoung Jan 30, 2024
f4d29b1
adjusted versions
erinyoung Jan 31, 2024
686ae17
adjusted versions
erinyoung Jan 31, 2024
e889c90
simplified inputs
erinyoung Jan 31, 2024
bf4609c
testing gbk files
erinyoung Jan 31, 2024
2ad22d4
adjusted label
erinyoung Jan 31, 2024
f240700
fixed summary
erinyoung Jan 31, 2024
f42f689
simplified multiqc
erinyoung Jan 31, 2024
37381c8
version to container
erinyoung Jan 31, 2024
a5a80af
adjusted labels
erinyoung Jan 31, 2024
7baf838
uncommented error strategy
erinyoung Jan 31, 2024
3eaa067
added version
erinyoung Jan 31, 2024
934d6ec
changed to gff
erinyoung Jan 31, 2024
4ec7332
added header
erinyoung Jan 31, 2024
ff688c1
moved sorted_matrix
erinyoung Jan 31, 2024
175e84b
adjusted header
erinyoung Jan 31, 2024
787e19f
fixed input
erinyoung Jan 31, 2024
becf61e
fixed inputs
erinyoung Jan 31, 2024
dc64a6b
updated to 2.2.2.7
erinyoung Jan 31, 2024
8597e39
moved back to gff
erinyoung Jan 31, 2024
39002a4
removed meta
erinyoung Jan 31, 2024
9e641b6
adjusted label resource management
erinyoung Jan 31, 2024
cc2bef3
added versions channel
erinyoung Jan 31, 2024
6178f00
added versions channel
erinyoung Jan 31, 2024
014656a
added versions channel
erinyoung Jan 31, 2024
5414448
initial versions added
erinyoung Jan 31, 2024
cbe8398
initial versions added
erinyoung Jan 31, 2024
94c5f59
python script for files
erinyoung Jan 31, 2024
c0831ba
adjusting mash
erinyoung Feb 3, 2024
638c0bd
added core genome
erinyoung Feb 3, 2024
f040bec
changed text
erinyoung Feb 3, 2024
a35f226
remove genome_accessions
erinyoung Feb 3, 2024
bb016dd
made results optional
erinyoung Feb 3, 2024
d853ee3
fixed version parsing
erinyoung Feb 3, 2024
105c081
fixed version parsing
erinyoung Feb 3, 2024
99f6081
fixed version parsing
erinyoung Feb 3, 2024
76a4dbb
fixed version parsing
erinyoung Feb 3, 2024
d6645ea
for drprg
erinyoung Feb 3, 2024
6d5fcb8
fixed prefix
erinyoung Feb 3, 2024
ec17d2d
updated to 1.19
erinyoung Feb 3, 2024
38f5472
added length file
erinyoung Feb 3, 2024
dfad59a
fixed version parsing
erinyoung Feb 3, 2024
3a9d917
added all
erinyoung Feb 3, 2024
67e16d6
added mqc_prep and json_convert
erinyoung Feb 3, 2024
619763e
fixed version parsing
erinyoung Feb 3, 2024
0ea874b
added fastani_len_summary
erinyoung Feb 3, 2024
18c45b4
removed first
erinyoung Feb 3, 2024
06a5dca
removed first
erinyoung Feb 3, 2024
0db7349
added TODO
erinyoung Feb 3, 2024
7a1fc67
removed first
erinyoung Feb 3, 2024
07384d9
added mqc_prep
erinyoung Feb 3, 2024
b006977
removed first
erinyoung Feb 3, 2024
2bc640a
added drprg elgato emmtyper etc
erinyoung Feb 13, 2024
83c1d79
added kaptive
erinyoung Feb 13, 2024
bdda46a
fixed emit
erinyoung Feb 13, 2024
d3841de
added first
erinyoung Feb 13, 2024
c21001f
added first
erinyoung Feb 13, 2024
75fcbd0
added first
erinyoung Feb 13, 2024
84d8477
added first
erinyoung Feb 13, 2024
63b0d96
added first
erinyoung Feb 13, 2024
5469c79
removed comment
erinyoung Feb 13, 2024
48da847
added kaptive, fixed drprg summary
erinyoung Feb 13, 2024
d1c701f
adjusting memory reqs
erinyoung Feb 13, 2024
9408d6d
added config file and adjusted results
erinyoung Feb 13, 2024
f45d9e6
uncommented errorstrategy
erinyoung Feb 13, 2024
250b4cb
added path to files
erinyoung Feb 13, 2024
a8b8f7e
reduced memory
erinyoung Feb 13, 2024
5c01154
added fasta list
erinyoung Feb 13, 2024
7ae81e1
testing adding fastani ref
erinyoung Feb 13, 2024
fdee4f5
testing sample sheet and skip extras
erinyoung Feb 13, 2024
6029fda
fixed skipping extras
erinyoung Feb 13, 2024
5c64e68
fixed typos
erinyoung Feb 14, 2024
95a1900
check contigs instead of summary
erinyoung Feb 14, 2024
e312055
removed retry
erinyoung Feb 14, 2024
38c5cfe
find kleborate
erinyoung Feb 14, 2024
c327600
removed todo
erinyoung Feb 14, 2024
b37e492
redid fastani
erinyoung Feb 14, 2024
88b631d
unused
erinyoung Feb 14, 2024
2b476aa
added sra accessions
erinyoung Feb 14, 2024
eb31418
added versions removed script
erinyoung Feb 14, 2024
fb543e5
now keeping cseq and useq
erinyoung Feb 14, 2024
01bfe4c
download files from ena
erinyoung Feb 14, 2024
b75196f
moved where ch_versions
erinyoung Feb 14, 2024
657d983
removed legsta
erinyoung Feb 14, 2024
eed4372
removed todo
erinyoung Feb 14, 2024
5c1ecb2
added sra accessions
erinyoung Feb 14, 2024
11c7bf8
redid tests, added test0
erinyoung Feb 14, 2024
62e4a9c
added meta to channel
erinyoung Feb 14, 2024
b799941
removed roary
erinyoung Feb 15, 2024
e32c5a7
removed cat final file
erinyoung Feb 15, 2024
2c2392e
fixed tabs
erinyoung Feb 15, 2024
9cec6b2
update to checkout v4
erinyoung Feb 15, 2024
bf4ae0e
increased to process high
erinyoung Feb 15, 2024
f2f3f01
fixed tab
erinyoung Feb 15, 2024
4072652
add if to mashtree
erinyoung Feb 15, 2024
f4133db
added circulocov and blobtools
erinyoung Feb 22, 2024
0aad9b4
added circulocov and blobtools
erinyoung Feb 22, 2024
5dfd679
added blast
erinyoung Feb 22, 2024
430ba20
added version
erinyoung Feb 22, 2024
e7a5a3e
added version
erinyoung Feb 22, 2024
7c3c4e0
added blobtools and quality assessment
erinyoung Feb 22, 2024
5847a41
added first
erinyoung Feb 22, 2024
2613756
removed process not species specific
erinyoung Feb 22, 2024
1c329a8
non-species processes
erinyoung Feb 22, 2024
6ec4f6c
added circulocov
erinyoung Feb 22, 2024
c393c12
fixed typos for NA
erinyoung Feb 22, 2024
6bbdc5d
adding information back in
erinyoung Feb 22, 2024
3f112d4
added space between letters
erinyoung Feb 22, 2024
6a33722
adjusted hidden
erinyoung Feb 22, 2024
5cd9634
removed UPHLICA
erinyoung Feb 22, 2024
60f1752
added groupTuple back
erinyoung Feb 22, 2024
c7e0f8c
uncommented errorStrategy
erinyoung Feb 22, 2024
ea6eaab
adjusted params
erinyoung Feb 22, 2024
3d4c000
added param file for config
erinyoung Feb 22, 2024
175a4fe
added nextflow -version
erinyoung Feb 23, 2024
5f83be9
added tools
erinyoung Feb 23, 2024
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added sra accessions
  • Loading branch information
erinyoung committed Feb 14, 2024
commit 5c1ecb2a3b58539b197d21938e98cb57f4a54637
3 changes: 1 addition & 2 deletions subworkflows/min_hash.nf
Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,9 @@ workflow min_hash {
ch_mash_sketches = Channel.empty()
ch_versions = Channel.empty()

if ( params.sample_sheet || params.reads ) {
if ( params.sample_sheet || params.reads || params.sra_accessions ) {
mash_sketch_fastq(ch_reads)

// TODO : test mash_err
mash_err(mash_sketch_fastq.out.err)

ch_mash_sketches = ch_mash_sketches.mix(mash_sketch_fastq.out.msh.filter({it[1].size() > 0 }))
Expand Down