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Nf phage finder #9

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merged 42 commits into from
Sep 23, 2024
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be57915
Early version. Not yet functional
aw-watson Jul 1, 2024
b476074
IDBA runs from NF script
aw-watson Jul 2, 2024
f91da30
4 of 5 assemblers running
aw-watson Jul 3, 2024
ef415fe
all assemblers running
aw-watson Jul 5, 2024
b939da8
Assemblers running. Graphs produced.
aw-watson Jul 8, 2024
3333575
workflow now creates contigs for assembly
aw-watson Jul 9, 2024
1a51cb3
Docker image for environment
aw-watson Jul 12, 2024
53aa4b1
Reduced Docker image size: 2.87GB->1.3GB
aw-watson Jul 15, 2024
1d8d2a6
initial NF version
aw-watson Jul 16, 2024
5bf8798
runFaQCs now uses multistage build
aw-watson Jul 16, 2024
fa8188b
added test files in central location
aw-watson Jul 16, 2024
7f29a88
minor revisions
aw-watson Jul 17, 2024
2dc63d7
variable definition
aw-watson Jul 17, 2024
4fdb0b0
third-party requirement rework
aw-watson Jul 17, 2024
c675ddf
charliecloud now used to run sra2fastq and runFaQCs
aw-watson Jul 22, 2024
fd09340
readsToContig now uses Charliecloud
aw-watson Jul 22, 2024
938e03a
taxonomy classification running against databases
Jul 25, 2024
af4bb0b
Initial Dockerfile
aw-watson Jul 26, 2024
8fd6f09
v1.0 Docker image
aw-watson Jul 29, 2024
e12522e
shifted execution of Krona prep scripts to workflow
aw-watson Jul 29, 2024
0634ccc
attempt to resolve singularity write permissions
aw-watson Jul 30, 2024
3645606
Better matches EDGE output
aw-watson Aug 7, 2024
b2c3d5f
Attempts to rescue incomplete assemblies, similar to EDGE
aw-watson Aug 8, 2024
4ecb0ab
properly creates container converted to Singularity
aw-watson Aug 12, 2024
463fcf3
Runs all taxonomies in container
aw-watson Aug 14, 2024
c2af310
fixed scripts to prevent container issues
aw-watson Aug 14, 2024
cc3bf97
Merge branch 'nf_readsTaxonomy' of https://github.com/LANL-Bioinforma…
aw-watson Aug 14, 2024
8ae4358
better matchingfor EDGE output
aw-watson Aug 15, 2024
b7b7d25
Fixed issue in perl scripts causing errors when generating reports
aw-watson Aug 22, 2024
d990ebb
Per discussions with Mark, prefer Singularity execution over Charliec…
aw-watson Aug 26, 2024
9f5ade8
Creating PDFs from SVGs
aw-watson Aug 26, 2024
a47ae79
producing PDFs from SVG trees
aw-watson Aug 26, 2024
0465aed
adding the actual svg2pdf script to bin
aw-watson Aug 26, 2024
85fc74d
Merge branch 'nf_readsTaxonomy' of https://github.com/LANL-Bioinforma…
aw-watson Aug 26, 2024
c97cf06
fixed heatmap generation
aw-watson Sep 3, 2024
7eb69e7
cleanup
aw-watson Sep 3, 2024
20f99cc
Merge pull request #6 from LANL-Bioinformatics/dockerReduction
mflynn-lanl Sep 16, 2024
8fa630c
Merge pull request #7 from LANL-Bioinformatics/nf_runAssembly
mflynn-lanl Sep 16, 2024
b111107
Merge pull request #8 from LANL-Bioinformatics/nf_readsTaxonomy
mflynn-lanl Sep 16, 2024
f3dc5b5
basic pipeline
aw-watson Sep 17, 2024
3c99563
working containerization
aw-watson Sep 18, 2024
5442168
Publishing with correct structure. Matches existing EDGE test results.
aw-watson Sep 18, 2024
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attempt to resolve singularity write permissions
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aw-watson committed Jul 30, 2024
commit 0634ccc77dc95c2d5d0762afb0c908599c268b17
7 changes: 5 additions & 2 deletions readsTaxonomyAssignment/nextflow.config
Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
docker.enabled=true
process.container = 'apwat/reads_taxonomy:1.0'
singularity.enabled=true
process.container = 'apwat/reads_taxonomy:1.1'
singularity {
runOptions="--writable-tmpfs --fakeroot"
}
params {
pairFile = "nf_assets/NO_FILE"
unpairFile = "nf_assets/NO_FILE2"
3 changes: 3 additions & 0 deletions readsTaxonomyAssignment/readsTaxonomyAssignment.nf
Original file line number Diff line number Diff line change
@@ -120,6 +120,9 @@ process readsTaxonomyConfig {
def np = (params.fastq_source != null && params.fastq_source.equalsIgnoreCase("nanopore")) ? "--nanopore " : ""

"""
mkdir -p /venv/opt/krona/taxonomy
touch /venv/opt/krona/taxonomy/taxdump.tar.gz
chmod 777 /venv/opt/krona/taxonomy/taxdump.tar.gz
updateTaxonomy.sh

updateAccessions.sh