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2.1.0 release #161

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7dc9838
added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'
SandraBabirye Aug 15, 2024
0548d90
added two new nf-core modules 'agat/sptatistics and agat/sqstatbasic'
SandraBabirye Aug 15, 2024
cfafbaa
added new subworkflow to obtain annotation summary statistics
SandraBabirye Aug 15, 2024
ddc3edc
added params.annotation_set
SandraBabirye Aug 15, 2024
3bd733a
added documentation for params.annotation_set
SandraBabirye Aug 15, 2024
131b7b8
added annotation_stats as specific output directory
SandraBabirye Aug 15, 2024
e98a375
allocated resources for the two new processes 'AGAT-SPSTATISTICS and …
SandraBabirye Aug 15, 2024
5a2abe7
added new subworkflow and params.annotation_set
SandraBabirye Aug 15, 2024
c35db05
added path to the test annotation file
SandraBabirye Aug 15, 2024
2fc43e8
modified the file after running prettier
SandraBabirye Aug 15, 2024
a8dbd78
added a new subworkflow 'ANNOTATION_STATS)
SandraBabirye Aug 16, 2024
da91c57
Edited annotation_statistics.nf file
SandraBabirye Aug 16, 2024
65b463e
edited the pattern for --annotation_set to include gff rather than gff3
SandraBabirye Aug 16, 2024
85ac505
edited the pattern for --annotation_set to include gff rather than gff3
SandraBabirye Aug 16, 2024
7e201c7
Merge pull request #135 from sanger-tol/annotation_statistics
BethYates Aug 16, 2024
26bd58c
added a python script that extracts the relevant annotation statistic…
SandraBabirye Aug 29, 2024
fe3c78e
added a new local module to extract annotation statistics information
SandraBabirye Aug 29, 2024
fd0d992
edited the annotation_stats subworkflow to include the new local module
SandraBabirye Aug 29, 2024
e6c6778
adjusted the allocated memory for agat_spstatistics and agat_sqstatba…
SandraBabirye Aug 29, 2024
ead4298
edited the annotation_stats subworkflow to include the new local module
SandraBabirye Aug 29, 2024
a52bc5d
edited the annotation_stats subworkflow to include the new local module
SandraBabirye Aug 29, 2024
054dade
edited the annotation_stats subworkflow and removed .out
SandraBabirye Aug 29, 2024
0e316cd
edited the modules.confif file
SandraBabirye Aug 29, 2024
5902545
edited the file
SandraBabirye Aug 29, 2024
0f8b9ae
edited the file
SandraBabirye Aug 29, 2024
5b6db7a
edited file
SandraBabirye Aug 29, 2024
fe44659
edited file
SandraBabirye Aug 29, 2024
d715b26
edited file
SandraBabirye Aug 29, 2024
9b21ccf
edited file
SandraBabirye Aug 29, 2024
5735681
edited file
SandraBabirye Aug 29, 2024
ee54ce0
edited file
SandraBabirye Aug 29, 2024
af5ae87
edited file
SandraBabirye Aug 29, 2024
0b47a55
edited file
SandraBabirye Aug 29, 2024
9f6d570
edited file
SandraBabirye Aug 29, 2024
8276619
edited file
SandraBabirye Aug 29, 2024
71db7fb
edited file
SandraBabirye Aug 29, 2024
c442041
edited file
SandraBabirye Aug 29, 2024
65ce7b4
edited file
SandraBabirye Aug 29, 2024
8fc6d6a
edited file
SandraBabirye Aug 29, 2024
a86d691
edited file
SandraBabirye Aug 29, 2024
2993e06
edited file
SandraBabirye Aug 29, 2024
1e5066f
edited the input channels
SandraBabirye Aug 29, 2024
38edfb1
created a tuple to extract meta id and file path
SandraBabirye Aug 29, 2024
db4f0a2
edited output channel
SandraBabirye Aug 29, 2024
269e1f3
removal of the full publishDir block for both of the nf-core AGAT pro…
SandraBabirye Aug 29, 2024
5ac5e4b
edited the output channel
SandraBabirye Aug 29, 2024
54c908d
edited the output file name
SandraBabirye Aug 29, 2024
c40cb4f
edited the output file name
SandraBabirye Aug 29, 2024
1f10c83
edited the output file and input channels
SandraBabirye Sep 3, 2024
886fc6e
edited the output file
SandraBabirye Sep 3, 2024
601abc7
edited the file permisions
SandraBabirye Sep 3, 2024
b0c4490
edited the annotation_statistics.nf file
SandraBabirye Sep 3, 2024
2fcca2c
Fix code formatting with Black
SandraBabirye Sep 3, 2024
77c6d5e
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
fd7ca06
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
09630ed
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
f94429e
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
093c653
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
f2d479a
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
6f12169
Fix EditorConfig linting issues
SandraBabirye Sep 3, 2024
b053f15
edited the ch_versions for AGAT_SPSTATISTICS
SandraBabirye Sep 4, 2024
57eec24
Merge pull request #136 from SandraBabirye/annotation_statistics
BethYates Sep 4, 2024
e0f5a8c
added gffread nf-core module
SandraBabirye Sep 18, 2024
b339b7a
added busco to run in protein mode
SandraBabirye Sep 18, 2024
c3336b2
added input channel ch_fasta to subworkflow ANNOTATION_STATS
SandraBabirye Sep 18, 2024
e7e15f6
edited the input channels for the BUSCO process
SandraBabirye Sep 18, 2024
18f07a8
added the protein mode
SandraBabirye Sep 18, 2024
e69d60e
added the lineage_db as input channel for the ANNOTATION_STATS subwor…
SandraBabirye Sep 18, 2024
ce859c0
edited the input channels for BUSCO
SandraBabirye Sep 18, 2024
c64153e
added an input channel for busco stats in the local module
SandraBabirye Sep 18, 2024
9f6870e
edited input channels for the ANNOTATION_STATS subworkflow
SandraBabirye Sep 18, 2024
1813b2d
edited input channels for the ANNOTATION_STATS subworkflow
SandraBabirye Sep 18, 2024
0e9fdbc
edited input channels for the ANNOTATION_STATS subworkflow
SandraBabirye Sep 18, 2024
554f1c5
edited the file to extract fasta file path
SandraBabirye Sep 18, 2024
6a39117
edited the file to extract fasta file path
SandraBabirye Sep 18, 2024
6bad994
edited the input channel for the extract annotation statistics local …
SandraBabirye Sep 18, 2024
7c4c496
removed the trailing white space
SandraBabirye Sep 18, 2024
7fe58fc
added -y argument to the GFFREAD process
SandraBabirye Sep 23, 2024
21f95b7
Update CITATION.cff
tkchafin Oct 11, 2024
39b6690
Merge pull request #147 from sanger-tol/spelling
tkchafin Oct 11, 2024
bc7809f
edited files
SandraBabirye Oct 23, 2024
6db6859
edited the file to run busco in protein mode
SandraBabirye Oct 23, 2024
1feb2a6
edited python script to include the busco stats file
SandraBabirye Oct 23, 2024
ee4e2a9
edited files
SandraBabirye Oct 23, 2024
21f2b4d
edited files
SandraBabirye Oct 23, 2024
64a39d5
fixed black linting issues
SandraBabirye Oct 23, 2024
8e5490c
added a busco stats file as parameter
SandraBabirye Oct 23, 2024
208e3ab
edited the arguments
SandraBabirye Oct 23, 2024
b060f6e
fixing black linting issues
SandraBabirye Oct 23, 2024
80301fe
edited the python script to extract busco stats
SandraBabirye Oct 25, 2024
f4d28c7
edited the input channels for buscoproteins process
SandraBabirye Oct 25, 2024
d95f4b5
Changed the order of inputs for ANNOTATION_STATS
SandraBabirye Oct 25, 2024
164b74d
edited the busco output file channel to json
SandraBabirye Oct 25, 2024
99a6e26
edited the python script to extract the one_line_summary information …
SandraBabirye Oct 25, 2024
dfdb0cf
Updated annotation_statistics.nf file
SandraBabirye Oct 25, 2024
fbc3deb
fixing black issues
SandraBabirye Oct 25, 2024
af3a412
fixing linting issues
SandraBabirye Oct 25, 2024
7acb7b8
remove trailing whitespace
SandraBabirye Oct 25, 2024
5ad88dd
removed the left padding space
SandraBabirye Oct 25, 2024
cf1e9d1
removed the left padding space
SandraBabirye Oct 25, 2024
067833c
updated modules.config
SandraBabirye Oct 25, 2024
05114c8
Merge pull request #142 from SandraBabirye/busco_feature
BethYates Oct 31, 2024
0ebe932
Merge branch 'annotation_stats_dev' into public_dev
BethYates Nov 1, 2024
7a08874
Added annotation statistics to the full parameter list and genomenote…
BethYates Nov 13, 2024
37b9838
typo
BethYates Nov 13, 2024
70a80b8
corrected some of the statistics being being returned, we should be …
BethYates Nov 14, 2024
96cf0bd
updated docs to include annotation statistics subworkflow
BethYates Nov 14, 2024
06e2b20
prettier fixes
BethYates Nov 14, 2024
fb20ba4
Query Ensembl's new metadata API to determine if this assembly has be…
BethYates Nov 14, 2024
d2a5b17
documentation updates
BethYates Nov 14, 2024
3f52746
black fix
BethYates Nov 14, 2024
3490b8e
switch to beta url as ensembl rapid site data is now frozen and all d…
BethYates Nov 15, 2024
6a12288
query by taxon_id rather than species name
BethYates Nov 19, 2024
019e9ae
updated comments/usage to refelect change to querying using taxon_id …
BethYates Nov 19, 2024
a343c27
deleted empty file
BethYates Nov 19, 2024
748a325
fixed typo
BethYates Nov 19, 2024
14614fb
modified output file name and directory of annotation_statistics subw…
BethYates Nov 19, 2024
3db5b58
Merge pull request #151 from sanger-tol/add_ensembl_metadata_check
BethYates Nov 20, 2024
5418341
Merge branch 'dev' into public_dev
BethYates Nov 20, 2024
c4f45a0
Merge pull request #150 from sanger-tol/public_dev
BethYates Nov 20, 2024
ae8db5c
Updated docs ahead of release
BethYates Nov 20, 2024
d61696d
updated nf-core/agat modules
tkchafin Nov 22, 2024
6cc12cd
update nf-core/bamtobed
tkchafin Nov 22, 2024
13687d9
nf-core/busco updated to 5.7.1 and patched
tkchafin Nov 22, 2024
798369b
nf-core/cooler updated
tkchafin Nov 22, 2024
c9e4211
nf-core/dumpsoftwareversions updated
tkchafin Nov 22, 2024
061ac2e
nf-core/gffread updated
tkchafin Nov 22, 2024
1f18dad
nf-core module updates
tkchafin Nov 23, 2024
bd8bfaa
nf-core module updates
tkchafin Nov 25, 2024
dd58ec1
remove anaconda references
tkchafin Nov 25, 2024
4a86006
Merge pull request #153 from tkchafin/anaconda_purge
tkchafin Nov 25, 2024
f6220c0
nf-core samtools/view updated
tkchafin Nov 25, 2024
2930baf
Merge pull request #154 from tkchafin/anaconda_purge
tkchafin Nov 25, 2024
a01d592
remote deprecated cleanup=true
tkchafin Dec 5, 2024
2f5b69b
Update CHANGELOG.md
tkchafin Dec 5, 2024
c4e97c3
Update CHANGELOG.md
tkchafin Dec 5, 2024
5f89876
Merge pull request #155 from sanger-tol/anaconda_purge
tkchafin Dec 5, 2024
4eb4aa6
Merge branch 'dev' into Release-2.1.0
BethYates Dec 5, 2024
bbfada7
prettier fix
BethYates Dec 5, 2024
e448f75
Update Utils.groovy
tkchafin Dec 9, 2024
e11e4a8
Merge pull request #152 from sanger-tol/Release-2.1.0
tkchafin Dec 9, 2024
bf9e345
Update CHANGELOG.md
tkchafin Dec 9, 2024
8b9de0f
Merge pull request #158 from sanger-tol/changelog
tkchafin Dec 9, 2024
44f238e
removed merquryfk
tkchafin Dec 10, 2024
8add69e
prettier linting
tkchafin Dec 10, 2024
1092fdc
Merge pull request #160 from tkchafin/merquryfk
tkchafin Dec 13, 2024
974f5cc
Fixed the CI by switching to the v2 of the action
muffato Dec 13, 2024
ee78df8
Merge pull request #162 from sanger-tol/ci
tkchafin Dec 16, 2024
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edited file
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SandraBabirye committed Aug 29, 2024
commit 9b21ccf205cc9ba29d11ce353e37cd36ca905cb7
4 changes: 2 additions & 2 deletions subworkflows/local/annotation_statistics.nf
Original file line number Diff line number Diff line change
@@ -32,15 +32,15 @@ workflow ANNOTATION_STATS {
ch_versions = ch_versions.mix (basic_stats.versions.first() )

// Print basic_stats outputs to inspect
basic_stats.stats_txt.view { "Basic Stats TXT: ${it}" }
basic_stats.view { "Basic Stats TXT: ${it}" }


// Other feature stats e.g intron count & length etc
other_stats = AGAT_SPSTATISTICS(ch_unzipped)
ch_versions = ch_versions.mix ( other_stats.versions.first() )

// Print other_stats outputs to inspect
other_stats.stats_txt.view { "Other Stats TXT: ${it}" }
other_stats.view { "Other Stats TXT: ${it}" }

// Parsing the txt files as input for the local module
EXTRACT_ANNOTATION_STATISTICS_INFO(basic_stats.stats_txt, other_stats.stats_txt)