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Converting Galaxy wf to Nextflow wf #1

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Converting Galaxy wf to Nextflow wf #1

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fdd8dc0
Update main.nf - adding wf process names
anilthanki Oct 25, 2024
fb359c8
Update main.nf - populate Column_rearrange processes
anilthanki Oct 25, 2024
47d6662
Update main.nf - populate mergeGeneFiles
anilthanki Oct 25, 2024
f87d49b
add nextflow.config for Slurm
pmb59 Oct 25, 2024
7169e98
Update main.nf - moving input channels to workflow
anilthanki Oct 25, 2024
b7de140
Update main.nf - deleting redundant input channels
anilthanki Oct 25, 2024
aab1b63
Update main.nf - adds wf step for mergeGeneFile
anilthanki Oct 25, 2024
681aeb5
Update main.nf - adds workflow step for scanpy-read-10x
anilthanki Oct 25, 2024
4cec90b
Update main.nf - fixing typo
anilthanki Oct 25, 2024
9842c6a
Update main.nf - fixes input file names, process mergeGeneFiles and s…
anilthanki Oct 25, 2024
c23bb3a
removes duplicated process and renames a file
anilthanki Oct 28, 2024
2b039d0
populate scanpy_filter_cells process
anilthanki Oct 28, 2024
32731d0
replaes anndata file name with var
anilthanki Oct 28, 2024
9de5090
Populate scanpy_filter_genes process
anilthanki Oct 28, 2024
772d841
Adds missing quote
anilthanki Oct 28, 2024
f8ae27e
Populate normalise_data process
anilthanki Oct 28, 2024
c02a8c4
Populate normalise_data_internal process
anilthanki Oct 28, 2024
813c7ac
Populate find_variable_genes process
anilthanki Oct 28, 2024
418610e
Populate run_PCA process
anilthanki Oct 28, 2024
e3e74b0
Populate harmony_batch process
anilthanki Oct 28, 2024
9a23c62
Populate neighbours process
anilthanki Oct 28, 2024
e5e82e3
Applies batch_varibale
anilthanki Oct 28, 2024
458a7b4
Populate neighbours_for_umap process
anilthanki Oct 28, 2024
72c7473
removes random comment
anilthanki Oct 28, 2024
9632035
Fixes lint
anilthanki Oct 28, 2024
5272361
Fixes input for neighbours_for_umap
anilthanki Oct 28, 2024
fae78f8
Populate run_tsne process and fixes typo in neighbours_for_umap
anilthanki Oct 28, 2024
e960f6e
Populate run_UMAP process
anilthanki Oct 28, 2024
8342715
renames normalise_internal_data and adds container tag
anilthanki Oct 30, 2024
3cc4066
Update main.nf - fixing join command for needed output
anilthanki Oct 31, 2024
0d014f1
Update main.nf - sylink genes.tsv locally
anilthanki Oct 31, 2024
279b43c
Update main.nf - adding container tag and commenting param in filter…
anilthanki Oct 31, 2024
f874a37
Update nextflow.config - adding singularity param
anilthanki Oct 31, 2024
33f70da
Update main.nf - removing comment
anilthanki Oct 31, 2024
1c924fb
Update main.nf - adds container info fixes `batch_variable`
anilthanki Oct 31, 2024
48f5f8d
Update main.nf - fixes `batch_variable` condition, adds pca_param in …
anilthanki Oct 31, 2024
3f3fecb
edit process run_umap
pmb59 Nov 1, 2024
a94177a
edit process run_tsne
pmb59 Nov 1, 2024
12efb95
edit process neighbours_for_umap
pmb59 Nov 1, 2024
86de8ad
Update main.nf - fixes parallel run for neighbours_for_umap
anilthanki Nov 4, 2024
8bf90e9
Update main.nf - fixes process run_tsne
anilthanki Nov 4, 2024
b4d4ca2
fixes output run-tsne
Nov 4, 2024
fbf688e
Update main.nf - populate find_clusters process
anilthanki Nov 4, 2024
ad54b02
Update main.nf - fixes input for find_clusters
anilthanki Nov 4, 2024
310c5b2
add nf-core linting github action
pmb59 Nov 4, 2024
8e459d1
fix lint command
pmb59 Nov 4, 2024
cc5ea04
add java and nextflow to github action
pmb59 Nov 4, 2024
1651976
Update main.nf - adds more params and logs
anilthanki Nov 4, 2024
192ba0c
Update nextflow.config
anilthanki Nov 4, 2024
2a26c09
Mov away from nf-core pipeline check, we only want to check the synta…
pmb59 Nov 4, 2024
5591c44
Update main.nf - ignores failed run and keeps only successful run
anilthanki Nov 4, 2024
1900933
fix nextflow syntax check
pmb59 Nov 4, 2024
f184945
Update main.nf
anilthanki Nov 4, 2024
e0966f9
Update main.nf
anilthanki Nov 4, 2024
27359f6
Update main.nf - comments ignore error
anilthanki Nov 4, 2024
44b0e31
Update main.nf - fixed run_umap
anilthanki Nov 4, 2024
79b2127
Update main.nf - fixes run_umap
anilthanki Nov 4, 2024
a8319c1
Update main.nf - fixes run_umap
anilthanki Nov 4, 2024
06c13b6
add simplified ci config
pmb59 Nov 4, 2024
8a50a17
disable CIi for now to avoid noise
pmb59 Nov 4, 2024
19c6658
Update main.nf - adds parameter to neighbours_for_umap
anilthanki Nov 4, 2024
216a89f
Update main.nf - fixes neighbours_for_umap
anilthanki Nov 4, 2024
aa20bd6
Update main.nf - fixes neighbor spelling as per script name
anilthanki Nov 4, 2024
5b5a48b
Update main.nf - fixes run_umap for neighbor key
anilthanki Nov 4, 2024
cf621e5
fixes umap
Nov 5, 2024
806953a
populates find_markers process
Nov 5, 2024
8f32220
revert config changes
Nov 5, 2024
bbfc882
adds python script for final project process
Nov 5, 2024
b9b1189
Update nextflow-linter.yaml - adding back changes pushed by @pmadrgal
anilthanki Nov 5, 2024
d2b4a38
Fixed filter_gene and filter_cell connections
Nov 5, 2024
4b90e9f
changes permission
Nov 5, 2024
4961d5f
populate make_project_file process
Nov 5, 2024
d02f1a3
Update final_project.py - removing redundant code
anilthanki Nov 5, 2024
a010ff5
Update final_project.py - removes redundant code for uns_source files
anilthanki Nov 5, 2024
eb5a690
Update final_project.py - removes redundant obs_source operations
anilthanki Nov 6, 2024
814df0b
Update main.nf - adds container in make_project_file process
anilthanki Nov 6, 2024
376ad3a
Update final_project.py
anilthanki Nov 6, 2024
73eb167
Update main.nf - fixinf make_project_file process
anilthanki Nov 6, 2024
9063a30
Update nextflow.config
anilthanki Nov 6, 2024
0dc94e5
Update main.nf
anilthanki Nov 6, 2024
b8cb996
Update main.nf - now uses param `dir_path` param for input files
anilthanki Nov 6, 2024
9f512a9
Create data_prep.sh
anilthanki Nov 6, 2024
2000f30
Update data_prep.sh - fixing log and force unzip
anilthanki Nov 6, 2024
ee8b177
Update main.nf - adds results dir
anilthanki Nov 7, 2024
47b6395
Update nextflow.config - temp commenting lines from config file
anilthanki Nov 7, 2024
82408ae
Add draft processes and conditional for scrublet
irisdianauy Nov 7, 2024
1b5847d
Add param technology, change conditional
irisdianauy Nov 7, 2024
2b37608
Correct workflow
irisdianauy Nov 7, 2024
014601d
Rename scrublet process output
irisdianauy Nov 7, 2024
02501d9
Add real scrublet commands
irisdianauy Nov 8, 2024
8b74c49
Initialise batch variable, correct scrublet output format
irisdianauy Nov 8, 2024
ddb3916
Allow scrublet to execute without a batch variable
irisdianauy Nov 12, 2024
3ec2fe6
bash correction
irisdianauy Nov 12, 2024
55feac5
correct if expression
irisdianauy Nov 12, 2024
12f2024
Filter predicted doublets if applicable
irisdianauy Nov 13, 2024
130486f
Update main.nf - adds `restore_unscaled` process - not tested
anilthanki Nov 13, 2024
2e19d39
Create resource_unscalled.py
anilthanki Nov 13, 2024
b5e37d1
Update main.nf - adds missing `(`
anilthanki Nov 13, 2024
6bbf4cb
Update main.nf - adding `processed_file` back
anilthanki Nov 13, 2024
22d3728
Update main.nf - fixes `restore_unscaled`
anilthanki Nov 13, 2024
77b50c2
Update main.nf - addsmissin `}`
anilthanki Nov 13, 2024
9fd8361
Rename resource_unscalled.py to restore_unscaled.py
anilthanki Nov 13, 2024
75a57b0
Update main.nf - fixed mapping for `find_marker` after `restore_unsca…
anilthanki Nov 13, 2024
2b539b7
Update README.md
anilthanki Nov 13, 2024
db56ad6
Update main.nf - adds publishDir options..
anilthanki Nov 13, 2024
96881dd
Update main.nf - fixes err
anilthanki Nov 13, 2024
281875b
Update main.nf - fixes err
anilthanki Nov 13, 2024
6a2b736
Update main.nf - adds publishdir for scrublet plot
anilthanki Nov 13, 2024
6b19a64
Update main.nf - redirects output to `publishDir`
anilthanki Nov 15, 2024
040250c
Update main.nf
anilthanki Nov 15, 2024
82e3303
Update main.nf - removed filter_failed_umap/tsne as errorStrategy 'ig…
anilthanki Nov 15, 2024
73314b9
Update main.nf - `merge_embedings` removed as `TNSEs_ch.mix(UMAPs_ch)…
anilthanki Nov 15, 2024
7f9162f
Update main.nf - remove `filtered_cellgroup_markers` as `errorStrate…
anilthanki Nov 15, 2024
81b6e23
Update main.nf - `merge_collection` and `build_list` removed as its d…
anilthanki Nov 15, 2024
7c4c139
Update main.nf - removed `clustering_slot_names` and `merge_group_slo…
anilthanki Nov 15, 2024
c540cdf
Update main.nf - removed `meta_vars` it was galaxy specific function…
anilthanki Nov 15, 2024
bce8436
Update main.nf - removes hard coded name
anilthanki Nov 15, 2024
be5fcec
Update main.nf - adds missing `)`
anilthanki Nov 15, 2024
bbcb763
Update main.nf - adds `output_dir` param
anilthanki Nov 15, 2024
e81f6bc
Update README.md
anilthanki Nov 15, 2024
f32e525
Update data_prep.sh - adds optional output dir
anilthanki Nov 19, 2024
6c088d2
Update README.md - updates read me
anilthanki Nov 19, 2024
ea27bba
Update main.nf - removes redundant comma
anilthanki Nov 19, 2024
ffd6443
Update nextflow.config - adds config for reporting
anilthanki Nov 19, 2024
23f0b6c
Update nextflow.config - generates report in `result_dir_path` withou…
anilthanki Nov 20, 2024
7ed1533
Update main.nf - making `batch_variable` and `pca_param` as params.
anilthanki Nov 20, 2024
52f75b3
Update main.nf - rename `pca_param` variable as `representation`
anilthanki Nov 20, 2024
deb5506
Update main.nf - renames output to match existing pipeline
anilthanki Nov 20, 2024
831982c
Update main.nf - parameterising container
anilthanki Nov 20, 2024
9c05d8e
Update main.nf - rename `scanpy_container` to `scanpy_scripts_container`
anilthanki Nov 20, 2024
05d3e75
Update README.md
anilthanki Nov 20, 2024
290d174
Update main.nf - rename output dir
anilthanki Nov 20, 2024
021411d
Update main.nf
anilthanki Nov 28, 2024
4a2af1f
Update main.nf
anilthanki Nov 28, 2024
5d568d9
make scripts executable
pmb59 Nov 29, 2024
cc29b1f
Update main.nf - renaming tsne and umap tsvs
anilthanki Dec 3, 2024
9b89d11
Update main.nf - updates output names
anilthanki Dec 3, 2024
2d4e7e3
Update main.nf
anilthanki Dec 3, 2024
de3c4f4
Update main.nf - updates cluster file name to match existing and pars…
anilthanki Dec 3, 2024
c300446
Update main.nf - fixes cluster output
anilthanki Dec 3, 2024
651119a
Update main.nf - changes marker file name
anilthanki Dec 4, 2024
a69967f
Update main.nf - ads log
anilthanki Dec 5, 2024
af972a3
Update main.nf - fixes marker rename
anilthanki Dec 5, 2024
df76b9f
Update main.nf - changes marker tsv name
anilthanki Dec 5, 2024
98ae08e
Update main.nf - correct key added in run_umap
irisdianauy Dec 6, 2024
6cb9451
add _n in embeddings_neighbors_n_
pmb59 Dec 6, 2024
c24f6e1
Update main.nf - adding log info
anilthanki Dec 10, 2024
0d3248c
Update main.nf - filter cell process n_counts based on technology
anilthanki Dec 10, 2024
7e61db3
Add process scale_data
irisdianauy Dec 11, 2024
2806466
reorder params.neighbor_values
pmb59 Dec 12, 2024
d420d39
Update main.nf
pmb59 Dec 12, 2024
38766ea
set env variable PYTHONIOENCODING = 'utf-8' for all processes
pmb59 Dec 12, 2024
18a690e
fix env PYTHONIOENCODING = 'utf-8'
pmb59 Dec 12, 2024
8aece46
Update main.nf
pmb59 Dec 12, 2024
9312311
ensure PYTHONIOENCODING='utf-8' on each scanpy-script command
pmb59 Dec 13, 2024
27503b5
upgrade scanpy-scripts
pmb59 Dec 18, 2024
ecdddb7
pin production version of scanpy-scripts
pmb59 Dec 18, 2024
c2a2852
upgrade s. scripts
pmb59 Dec 19, 2024
ef03cda
specify a Singularity cache directory
pmb59 Dec 20, 2024
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