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Release candidate for 1.4 #79

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merged 67 commits into from
Mar 4, 2024
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6bb052d
Added nf-core/fastq_trim_fastp_fastqc subworkflow
GallVp Feb 14, 2024
a88808a
Removed old HIC_PREPROCESS subworkflow
GallVp Feb 14, 2024
391011c
Updated fastqc and fastp versions
GallVp Feb 14, 2024
7fe4d3d
Now using nf-core/FASTA_EXPLORE_SEARCH_PLOT_TIDK
GallVp Feb 14, 2024
aa80bbb
Multiple changes, see CHANGELOG.md
GallVp Feb 19, 2024
f9f6a7d
Added versions snippet to additional tools
GallVp Feb 19, 2024
24151a6
Added nf-core/TEMPLATE
GallVp Feb 19, 2024
8198830
A basic workflow now running successfully
GallVp Feb 20, 2024
d4cc276
Updated README and removed release_assnouncments action
GallVp Feb 20, 2024
51f75d4
Fixed template issues
GallVp Feb 20, 2024
cd0e900
Cleared additional linting checks
GallVp Feb 20, 2024
5c03bab
Added CHANGELOG
GallVp Feb 20, 2024
4701ad4
Fixed linting
GallVp Feb 20, 2024
2f8b46a
Bumped nxf version to 23.04.0
GallVp Feb 20, 2024
74d9ea7
Updated pipeline upto gt/stat
GallVp Feb 20, 2024
4cee5d9
Added NCBI_FCS_ADAPTOR
GallVp Feb 20, 2024
96c82fd
Added NCBI_FCS_GX sub workflow
GallVp Feb 20, 2024
2717953
Added module assemblathon_stats
GallVp Feb 20, 2024
94b6761
Added ncbi_fcs_gx
GallVp Feb 21, 2024
ec4c33d
Added stub test to ci
GallVp Feb 21, 2024
75faf2e
Updated stub test config
GallVp Feb 21, 2024
64eebf3
Added fasta_busco_plot workflow
GallVp Feb 21, 2024
92c5da1
Added fasta_explore_search_plot_tidk subworkflow
GallVp Feb 21, 2024
d6ba080
Added fasta_ltrretriever_lai
GallVp Feb 22, 2024
43255b6
Added fasta_kraken2
GallVp Feb 22, 2024
1589033
Added fastq_trim_fastp_fastqc
GallVp Feb 23, 2024
f0bc5a6
Added FQ2HIC subworkflow
GallVp Feb 26, 2024
1b2632f
Removed numerous linting issues
GallVp Feb 26, 2024
1dd2e26
Added versions snippet to multiple modules
GallVp Feb 26, 2024
fa0b294
Fixed path in stub assemblysheet
GallVp Feb 26, 2024
fdd04ec
Added fasta_synteny sub workflow
GallVp Feb 27, 2024
a6eec71
Added createreport module
GallVp Feb 27, 2024
93e7715
Fixed version links in the report
GallVp Feb 27, 2024
9716c76
Only printing non-default params in the report
GallVp Feb 27, 2024
6240901
Added additional params to stub test config
GallVp Feb 27, 2024
294c4a2
Fixed linting issues
GallVp Feb 27, 2024
321de30
Fixed reporting issues
GallVp Feb 27, 2024
53ff084
Removed TODO from base.conf
GallVp Feb 27, 2024
27b746f
Updated authors in the license
GallVp Feb 27, 2024
efdac55
Moved file for profile test_full
GallVp Feb 27, 2024
0d85347
Fixed minor issues to support test_full
GallVp Feb 28, 2024
8aefa66
Added pfr profile and params
GallVp Feb 28, 2024
1321d59
Fixed a bug which caused lai to run with null assembly fasta
GallVp Feb 28, 2024
cb325c0
Added a test for invalid files
GallVp Feb 28, 2024
39f6854
Updated modules and subworkflows
GallVp Feb 28, 2024
66de124
Add tag uniqueness checks
GallVp Feb 28, 2024
c1426f1
Removed assemblyqc_report from main workflow
GallVp Feb 29, 2024
85c1278
Updated the usage doc
GallVp Feb 29, 2024
071be83
Added pfr/params.json
GallVp Feb 29, 2024
5fa2df8
Merge branch 'dev' of github.com:Plant-Food-Research-Open/assembly_qc…
GallVp Feb 29, 2024
a24177c
Merge branch 'dev' of github.com:Plant-Food-Research-Open/assembly_qc…
GallVp Feb 29, 2024
bfdce22
Fixed linting
GallVp Feb 29, 2024
7968784
Now allowing {1,2}.fq.gz pattern for hic
GallVp Feb 29, 2024
d714bf0
Fixed container paths
GallVp Feb 29, 2024
f13a9e5
Updated fasta_ltrretriever_lai
GallVp Feb 29, 2024
d335747
Updated usage doc
GallVp Mar 1, 2024
218a7ab
Fixed multi GX launch bug
GallVp Mar 1, 2024
05f6f4f
Fixed null db path bug
GallVp Mar 1, 2024
cbebbf7
Added parameters.md file
GallVp Mar 1, 2024
53c7528
Crossed out conda
GallVp Mar 1, 2024
e4d4289
Fixed output formatting
GallVp Mar 1, 2024
eb121bd
Formatted output figs
GallVp Mar 1, 2024
a4c6490
Updated docs and removed bugs in version capture for awk and grep
GallVp Mar 3, 2024
36f102f
Updated usage doc
GallVp Mar 3, 2024
17d4317
Updated docs
GallVp Mar 4, 2024
edfb576
Bumped version to 1.4
GallVp Mar 4, 2024
5f403db
Updated CHANGELOG
GallVp Mar 4, 2024
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Added pfr/params.json
  • Loading branch information
GallVp committed Feb 29, 2024

Verified

This commit was signed with the committer’s verified signature.
vkubiv Volodymyr Kubiv
commit 071be83d80c4b56d25233539c92e4d71c44386f8
4 changes: 4 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -6,3 +6,7 @@ results/
testing/
testing*
*.pyc

# PFR files
*.stdout
*.stderr
8 changes: 4 additions & 4 deletions assets/schema_input.json
Original file line number Diff line number Diff line change
@@ -14,13 +14,13 @@
},
"fasta": {
"type": "string",
"pattern": "^\\S+\\.f(ast|as|sa|na)?\\.gz$",
"errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(ast|as|sa|na)' or '.f(ast|as|sa|na).gz'"
"pattern": "^\\S+\\.f(a|asta|as|sa|na)(\\.gz)?$",
"errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(a|asta|as|sa|na)' or '.f(a|asta|as|sa|na).gz'"
},
"gff3": {
"type": "string",
"pattern": "^\\S+\\.gff(3)?\\.gz$",
"errorMessage": "GFF3 file path cannot contain spaces and must have extension '.gff.gz' or '.gff3.gz'"
"pattern": "^\\S+\\.gff(3)?(\\.gz)?$",
"errorMessage": "GFF3 file path cannot contain spaces and must have extension '.gff.gz', '.gff3.gz', '.gff' or '.gff3'"
},
"monoploid_ids": {
"errorMessage": "Monoploid IDs txt file path cannot contain spaces and must have extension '.txt'",
4 changes: 2 additions & 2 deletions assets/schema_xref_assemblies.json
Original file line number Diff line number Diff line change
@@ -14,8 +14,8 @@
},
"fasta": {
"type": "string",
"pattern": "^\\S+\\.f(ast|as|sa|na)?\\.gz$",
"errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(ast|as|sa|na)' or '.f(ast|as|sa|na).gz'"
"pattern": "^\\S+\\.f(a|asta|as|sa|na)(\\.gz)?$",
"errorMessage": "FASTA file path cannot contain spaces and must have extension '.f(a|asta|as|sa|na)' or '.f(a|asta|as|sa|na).gz'"
},
"synteny_labels": {
"errorMessage": "Synteny labels tsv path cannot contain spaces and must have extension '.tsv'",
29 changes: 29 additions & 0 deletions pfr/params.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
{
"input":"/workspace/assemblyqc/testdata/default/assemblysheet.csv",
"ncbi_fcs_adaptor_skip": false,
"ncbi_fcs_adaptor_empire": "euk",
"ncbi_fcs_gx_skip": false,
"ncbi_fcs_gx_tax_id": 3750,
"ncbi_fcs_gx_db_path": "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24",
"busco_skip": false,
"busco_mode": "geno",
"busco_lineage_datasets": "embryophyta_odb10 eudicots_odb10",
"busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc",
"tidk_skip": false,
"tidk_repeat_seq": "TTTAGGG",
"tidk_filter_by_size": true,
"tidk_filter_size_bp": 1000000,
"lai_skip": false,
"kraken2_skip": false,
"kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314",
"hic": null,
"synteny_skip": false,
"synteny_between_input_assemblies": true,
"synteny_many_to_many_align": false,
"synteny_max_gap": 1000000,
"synteny_min_bundle_size": 1000,
"synteny_plot_1_vs_all": true,
"synteny_color_by_contig": true,
"synteny_xref_assemblies": "/workspace/assemblyqc/testdata/default/xrefsheet.csv",
"outdir": "./results"
}
5 changes: 5 additions & 0 deletions pfr/profile.config
Original file line number Diff line number Diff line change
@@ -10,3 +10,8 @@ profiles {
}
}
}

params {
config_profile_name = 'Plant&Food profile'
config_profile_description = 'Plant&Food profile using SLURM in combination with Apptainer'
}
41 changes: 35 additions & 6 deletions pfr_assemblyqc
Original file line number Diff line number Diff line change
@@ -9,16 +9,45 @@
#SBATCH --error pfr_assemblyqc.stderr
#SBATCH --mem=4G

full_test_flag=0

# Parse command line options
while getopts "t" opt; do
case ${opt} in
t )
full_test_flag=1
;;
\? )
echo "Invalid option: $OPTARG" 1>&2
exit 1
;;
esac
done
shift $((OPTIND -1))

ml unload perl
ml apptainer/1.1
ml nextflow/23.04.4

export TMPDIR="/workspace/$USER/tmp"
export APPTAINER_BINDPATH="$APPTAINER_BINDPATH,$TMPDIR:$TMPDIR,$TMPDIR:/tmp"

nextflow \
main.nf \
-c pfr/profile.config \
-profile pfr,apptainer \
-resume \
--params-file pfr/params.json
if [ $full_test_flag -eq 1 ]; then
nextflow \
main.nf \
-c pfr/profile.config \
-profile pfr,apptainer,test_full \
--ncbi_fcs_gx_skip false \
--ncbi_fcs_gx_tax_id 35717 \
--ncbi_fcs_gx_db_path "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24" \
--kraken2_skip false \
--kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314" \
-resume
else
nextflow \
main.nf \
-c pfr/profile.config \
-profile pfr,apptainer \
-params-file pfr/params.json \
-resume
fi