broadinstitute/viral-pipelines-v2.1.33.8.zip
broadinstitute-viral-pipelines-31a7743
.coveragerc
384 Bytes
.dockstore.yml
14.4 kB
.gitattributes
33 Bytes
.github
workflows
build.yml
15.0 kB
.gitignore
1.1 kB
.readthedocs.yml
568 Bytes
.travis.yml
3.2 kB
LICENSE
2.1 kB
README.md
3.7 kB
docs
Makefile
6.8 kB
conf.py
9.6 kB
description.rst
3.7 kB
index.rst
466 Bytes
ncbi_submission.rst
8.6 kB
pipes-wdl.rst
634 Bytes
requirements.txt
73 Bytes
rulegraph.png
69.1 kB
viral-ngs-overview.png
243.0 kB
workflows.rst
607 Bytes
github_actions_ci
build-docs.sh
125 Bytes
build-dx.sh
2.8 kB
check-wdl-runtimes.sh
1.1 kB
dockstoreyml.sh
252 Bytes
install-pip-docs.sh
117 Bytes
install-wdl.sh
641 Bytes
list-docker-tags.sh
2.4 kB
relative-wdl-paths.sh
151 Bytes
tests-cromwell.sh
1.2 kB
tests-dx.sh
4.4 kB
tests-miniwdl.sh
2.2 kB
validate-wdl-womtool.sh
253 Bytes
version-wdl-runtimes.sh
537 Bytes
pipes
WDL
tasks
tasks_assembly.wdl
34.8 kB
tasks_demux.wdl
18.0 kB
tasks_interhost.wdl
8.5 kB
tasks_intrahost.wdl
12.9 kB
tasks_metagenomics.wdl
25.9 kB
tasks_ncbi.wdl
36.0 kB
tasks_ncbi_tools.wdl
20.2 kB
tasks_nextstrain.wdl
68.2 kB
tasks_read_utils.wdl
11.5 kB
tasks_reports.wdl
17.2 kB
tasks_sarscov2.wdl
28.2 kB
tasks_taxon_filter.wdl
8.6 kB
tasks_terra.wdl
4.2 kB
tasks_utils.wdl
19.0 kB
workflows
align_and_count.wdl
600 Bytes
align_and_count_multiple_report.wdl
1.5 kB
align_and_plot.wdl
1.8 kB
assemble_denovo.wdl
8.7 kB
assemble_refbased.wdl
11.6 kB
augur_export_only.wdl
635 Bytes
augur_from_assemblies.wdl
10.2 kB
augur_from_beast_mcc.wdl
1.5 kB
augur_from_mltree.wdl
5.0 kB
augur_from_msa.wdl
7.0 kB
bams_multiqc.wdl
797 Bytes
beast_gpu.wdl
503 Bytes
classify_kaiju.wdl
563 Bytes
classify_kraken2.wdl
650 Bytes
classify_krakenuniq.wdl
1.1 kB
classify_multi.wdl
7.0 kB
classify_single.wdl
4.8 kB
contigs.wdl
1.9 kB
coverage_table.wdl
280 Bytes
demux_deplete.wdl
9.2 kB
demux_metag.wdl
5.9 kB
demux_only.wdl
1.2 kB
demux_plus.wdl
4.7 kB
deplete_only.wdl
798 Bytes
detect_cross_contamination.wdl
3.1 kB
detect_cross_contamination_precalled_vcfs.wdl
1.6 kB
diff_genome_sets.wdl
738 Bytes
downsample.wdl
432 Bytes
fastq_to_ubam.wdl
413 Bytes
fetch_annotations.wdl
451 Bytes
fetch_sra_to_bam.wdl
1.3 kB
filter_classified_bam_to_taxa.wdl
895 Bytes
filter_sequences.wdl
308 Bytes
genbank.wdl
7.2 kB
isnvs_lofreq.wdl
1.0 kB
isnvs_merge_to_vcf.wdl
1.1 kB
isnvs_one_sample.wdl
549 Bytes
kraken2_build.wdl
482 Bytes
mafft.wdl
569 Bytes
mafft_and_snp.wdl
2.4 kB
mafft_and_snp_annotated.wdl
2.8 kB
mafft_and_trim.wdl
835 Bytes
merge_bams.wdl
479 Bytes
merge_metagenomics.wdl
927 Bytes
merge_tar_chunks.wdl
499 Bytes
merge_vcfs.wdl
445 Bytes
merge_vcfs_and_annotate.wdl
1.1 kB
multiqc_only.wdl
366 Bytes
read_depths.wdl
710 Bytes
sarscov2_batch_relineage.wdl
3.6 kB
sarscov2_biosample_load.wdl
2.6 kB
sarscov2_data_release.wdl
6.2 kB
sarscov2_genbank.wdl
8.6 kB
sarscov2_genbank_ingest.wdl
953 Bytes
sarscov2_gisaid_ingest.wdl
1.7 kB
sarscov2_illumina_full.wdl
24.2 kB
sarscov2_lineages.wdl
1.6 kB
sarscov2_nextclade_multi.wdl
630 Bytes
sarscov2_nextstrain.wdl
8.7 kB
sarscov2_nextstrain_aligned_input.wdl
8.6 kB
sarscov2_sequencing_reports.wdl
1.4 kB
sarscov2_sra_to_genbank.wdl
12.6 kB
scaffold_and_refine.wdl
2.7 kB
subsample_by_metadata.wdl
394 Bytes
subsample_by_metadata_with_focal.wdl
4.5 kB
terra_table_to_tsv.wdl
379 Bytes
terra_update_assemblies.wdl
429 Bytes
trimal.wdl
387 Bytes
cromwell
cromwell.gcid-viral-seq.conf
2.9 kB
cromwell.local-github_actions.conf
4.6 kB
cromwell.local-travis.conf
4.6 kB
dnax
dx-defaults-assemble_denovo.json
291 Bytes
dx-defaults-classify_kaiju.json
263 Bytes
dx-defaults-classify_kraken2.json
184 Bytes
dx-defaults-classify_krakenuniq.json
203 Bytes
dx-defaults-classify_multi.json
402 Bytes
dx-defaults-contigs.json
275 Bytes
dx-defaults-demux_metag.json
584 Bytes
dx-defaults-demux_plus.json
514 Bytes
dx-defaults-deplete_only.json
219 Bytes
dx-defaults-filter_classified_bam_to_taxa.json
120 Bytes
dx-extras.json
146 Bytes
dx-launcher
.gitignore
10 Bytes
README.md
1.8 kB
consolidate_run_tarballs.yml
1.8 kB
demux_launcher.yml
10.1 kB
dx-yml-build
833 Bytes
requirements-modules.txt
393 Bytes
test
input
5kb_human_from_chr6.fasta
5.1 kB
G5012.3.fasta
19.2 kB
G5012.3.mini.bam
381.1 kB
G5012.3.subset.bam
17.1 kB
G5012.3.testreads.bam
1.6 MB
LASV_NGA_2018_0026.fasta
10.3 kB
LASV_NGA_2018_0097.fasta
10.9 kB
LASV_NGA_2018_0541.fasta
10.6 kB
MA_MGH_00003.fasta
30.4 kB
MA_MGH_00004.fasta
30.4 kB
MA_MGH_00005.fasta
30.4 kB
WDL
cromwell-local
test_inputs-assemble_refbased-local.json
43 Bytes
test_inputs-augur_from_assemblies-local.json
47 Bytes
test_inputs-classify_kraken2-local.json
42 Bytes
test_inputs-fastq_to_ubam-local.json
39 Bytes
test_inputs-genbank-local.json
1.4 kB
miniwdl-local
test_inputs-align_and_plot-local.json
40 Bytes
test_inputs-assemble_denovo-local.json
41 Bytes
test_inputs-assemble_refbased-local.json
43 Bytes
test_inputs-augur_from_assemblies-local.json
47 Bytes
test_inputs-augur_from_beast_mcc-local.json
46 Bytes
test_inputs-classify_kraken2-local.json
42 Bytes
test_inputs-fastq_to_ubam-local.json
39 Bytes
test_inputs-genbank-local.json
1.5 kB
test_inputs-sarscov2_lineages-local.json
43 Bytes
test_outputs-assemble_denovo-local.json
42 Bytes
test_outputs-assemble_refbased-local.json
44 Bytes
test_outputs-sarscov2_lineages-local.json
44 Bytes
test_inputs-align_and_plot-local.json
246 Bytes
test_inputs-assemble_denovo-dnanexus.dx.json
761 Bytes
test_inputs-assemble_denovo-local.json
378 Bytes
test_inputs-assemble_refbased-local.json
201 Bytes
test_inputs-augur_from_assemblies-local.json
849 Bytes
test_inputs-augur_from_beast_mcc-local.json
165 Bytes
test_inputs-beast_gpu-local_nonauto.json
76 Bytes
test_inputs-classify_kraken2-local.json
264 Bytes
test_inputs-classify_multi-dnanexus.dx.json
636 Bytes
test_inputs-demux_plus-dnanexus.dx.json
934 Bytes
test_inputs-fastq_to_ubam-local.json
237 Bytes
test_inputs-genbank-local.json
1.5 kB
test_inputs-sarscov2_lineages-local.json
72 Bytes
test_outputs-assemble_denovo-local.json
585 Bytes
test_outputs-assemble_refbased-local.json
839 Bytes
test_outputs-sarscov2_lineages-local.json
213 Bytes
beast-lasv.tree
353.5 kB
beast-mers-auspice_config.json
662 Bytes
beast-mers-mcc.tree
272.5 kB
beast-simple-ebov-20k.xml
960.7 kB
clipDb.fasta
18.9 kB
ebov-makona.fasta
19.2 kB
genbank
KM821997.1.fasta
7.5 kB
KM821997.1.tbl
232 Bytes
KM821998.1.fasta
3.6 kB
KM821998.1.tbl
255 Bytes
MN908947.3.fasta
30.4 kB
MN908947.3.tbl
1.3 kB
author_template.sbt.j2
2.5 kB
authors-nga_lasv.sbt
9.7 kB
biosample-attributes-lasv.txt
21.5 kB
biosample-map-lasv-2018-RUN1.txt
1.0 kB
coverage-ma_mgh.txt
14.7 kB
coverage_report-RUN1-new_names.txt
2.7 kB
coverage_report-RUN1-workflow.txt
1.1 kB
default_sbt_values.yaml
1.1 kB
expected
LASV_NGA_2018_0026-1.cmt
260 Bytes
LASV_NGA_2018_0026-1.fsa
7.0 kB
LASV_NGA_2018_0026-1.gbf
14.7 kB
LASV_NGA_2018_0026-1.sqn
30.3 kB
LASV_NGA_2018_0026-1.src
324 Bytes
LASV_NGA_2018_0026-1.tbl
228 Bytes
LASV_NGA_2018_0026-1.val
2.1 kB
LASV_NGA_2018_0026-2.cmt
260 Bytes
LASV_NGA_2018_0026-2.fsa
3.4 kB
LASV_NGA_2018_0026-2.gbf
8.6 kB
LASV_NGA_2018_0026-2.sqn
25.0 kB
LASV_NGA_2018_0026-2.src
343 Bytes
LASV_NGA_2018_0026-2.tbl
203 Bytes
LASV_NGA_2018_0026-2.val
300 Bytes
LASV_NGA_2018_0097-1.cmt
263 Bytes
LASV_NGA_2018_0097-1.fsa
7.4 kB
LASV_NGA_2018_0097-1.gbf
15.2 kB
LASV_NGA_2018_0097-1.sqn
30.3 kB
LASV_NGA_2018_0097-1.src
324 Bytes
LASV_NGA_2018_0097-1.tbl
180 Bytes
LASV_NGA_2018_0097-1.val
0 Bytes
LASV_NGA_2018_0097-2.cmt
263 Bytes
LASV_NGA_2018_0097-2.fsa
3.5 kB
LASV_NGA_2018_0097-2.gbf
8.7 kB
LASV_NGA_2018_0097-2.sqn
25.2 kB
LASV_NGA_2018_0097-2.src
343 Bytes
LASV_NGA_2018_0097-2.tbl
203 Bytes
LASV_NGA_2018_0097-2.val
0 Bytes
LASV_NGA_2018_0541-1.cmt
261 Bytes
LASV_NGA_2018_0541-1.fsa
7.3 kB
LASV_NGA_2018_0541-1.gbf
15.1 kB
LASV_NGA_2018_0541-1.sqn
30.1 kB
LASV_NGA_2018_0541-1.src
324 Bytes
LASV_NGA_2018_0541-1.tbl
178 Bytes
LASV_NGA_2018_0541-1.val
306 Bytes
LASV_NGA_2018_0541-2.cmt
259 Bytes
LASV_NGA_2018_0541-2.fsa
3.4 kB
LASV_NGA_2018_0541-2.gbf
8.6 kB
LASV_NGA_2018_0541-2.sqn
25.5 kB
LASV_NGA_2018_0541-2.src
343 Bytes
LASV_NGA_2018_0541-2.tbl
251 Bytes
LASV_NGA_2018_0541-2.val
0 Bytes
genbank-sample_meta_src-lasv-2018-RUN1_v2.txt
15.3 kB
sars-cov-2_attributes_updated.txt
198.1 kB
in1.fastq
113 Bytes
in2.fastq
113 Bytes
kraken2_db-tinytest.tar.zst
44.4 kB
krona.taxonomy-20200505.tab.zst
16.7 MB
ref-lasv-ISTH2376.fasta
11.0 kB
zika-tutorial
README.md
303 Bytes
config
auspice_config.json
956 Bytes
colors.tsv
854 Bytes
dropped_strains.txt
672 Bytes
lat_longs.tsv
537 Bytes
zika_outgroup.gb
21.5 kB
data
KX369547.1.fna
11.1 kB
metadata.tsv
10.8 kB
sequences.fasta
361.3 kB
travis
build-docs.sh
125 Bytes
build-dx.sh
2.8 kB
check-wdl-runtimes.sh
1.2 kB
dockstoreyml.sh
252 Bytes
install-pip-docs.sh
117 Bytes
install-wdl.sh
641 Bytes
list-docker-tags.sh
2.4 kB
relative-wdl-paths.sh
151 Bytes
tests-cromwell.sh
1.2 kB
tests-dx.sh
4.4 kB
tests-miniwdl.sh
2.2 kB
validate-wdl-womtool.sh
253 Bytes
version-wdl-runtimes.sh
526 Bytes