broadinstitute viral-pipelines issues

broadinstitute / viral-pipelines

viral-ngs: complete pipelines

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attempt at fixing OpenBLAS-related nproc limit

#553 tomkinsc opened 3 weeks ago
0
demux_deplete small updates

#552 dpark01 closed 3 weeks ago
0
demux_deplete: make depletion optional, load biosample metadata to tables

#551 dpark01 closed 3 weeks ago
1
add grimer visualization to merge_metagenomics workflow

#550 dpark01 opened 1 month ago
0
limit GH build concurrency

#549 tomkinsc opened 1 month ago
0
bugfix dx deploy failures

#548 tomkinsc closed 1 month ago
0
scaffolding regression fixes plus docker updates

#547 dpark01 closed 1 month ago
1
documentation build fixes

#546 tomkinsc closed 1 month ago
2
Update polyphonia input parameters and defaults

#545 lakras closed 1 month ago
0
Adding Kraken to Krona conversion to blastoff.wdl

#544 golu099 opened 2 months ago
0
[bug] assemble_denovo fails at larger ANI distance

#543 dpark01 closed 4 weeks ago
1
bugfix fetch_sra_to_bam

#542 tomkinsc closed 3 months ago
0
add build environment spec to .readthedocs.yml config

#541 tomkinsc closed 3 months ago
0
increase default instance memory for kraken2 task 72 -> 90GB

#540 tomkinsc closed 3 months ago
0
in `create_or_update_sample_tables`, use the `sample_original` from demux as the key value for rows rather than `sample` (i.e. use IDs with forward slashes not dashes)

#539 tomkinsc opened 4 months ago
0
report reference genome length in align_reads output; use this value for assemble_refbased. reference_genome_length

#538 tomkinsc closed 3 months ago
1
add workflow to download multiple SRA accessions to multiple bams: fetch_multiple_sra_to_bams

#537 tomkinsc opened 4 months ago
0
classify_single: parameterize taxa to deplete

#536 dpark01 closed 4 months ago
0
guard against shell pipefails in align_and_count in instances where empty inputs would result in div-by-zero conditions

#535 tomkinsc closed 4 months ago
0
In align_and_count, change default to count only properly-paired reads

#534 tomkinsc opened 4 months ago
0
parameterize table names in create_or_update_sample_tables task

#533 tomkinsc opened 4 months ago
0
percolate biosample attributes to sample table in Terra

#532 dpark01 closed 3 weeks ago
0
update / make new Terra-friendly genbank prep workflow

#531 dpark01 opened 5 months ago
1
update nextclade 2 -> 3

#530 dpark01 opened 5 months ago
0
Reference selection improvements and nextclade generalization

#529 dpark01 closed 5 months ago
0
scaffolding and reference selection based on ANI

#528 dpark01 closed 5 months ago
1
update viral-core 2.3.0 -> 2.3.1

#527 tomkinsc closed 6 months ago
1
build and container updates

#526 dpark01 closed 6 months ago
0
expanded parameterization of align_and_count and additional output metrics

#525 tomkinsc closed 6 months ago
0
scaffold_and_refine_multitaxa -- more thorough assembly outputs

#524 dpark01 closed 6 months ago
0
WDL code/style cleanups

#523 dpark01 closed 6 months ago
1
update docker for try/except block with new error message

#522 jpramosbarroso closed 6 months ago
0
create_enterics_qc_viz simplify and improve portability

#521 jpramosbarroso closed 6 months ago
2
update personal branch

#520 jpramosbarroso closed 6 months ago
0
speed up data localization for certain tasks

#519 dpark01 closed 6 months ago
0
allow additional options for picard in FastqToUBAM

#518 tomkinsc closed 6 months ago
0
Make create_enterics_qc_viz whitespace tolerant

#517 dpark01 closed 6 months ago
0
update enterics visualization docker image

#516 jpramosbarroso closed 7 months ago
0
integrating threshold file

#515 jpramosbarroso closed 7 months ago
0
Fixing duplicate inputs bug

#514 jpramosbarroso closed 7 months ago
2
Visualization HTML PR

#513 jpramosbarroso closed 7 months ago
2
dockstore updates

#512 dpark01 closed 7 months ago
0
more scaffolding updates

#511 dpark01 closed 7 months ago
0
mark check_terra_env task as volatile

#510 tomkinsc closed 7 months ago
0
assemble_refbased aligns 0 reads

#509 marnieya closed 6 months ago
5
include user email among outputs of check_terra_env task

#508 tomkinsc closed 7 months ago
0
add workflows to add to or create library and sample tables based on demultiplexing output

#507 tomkinsc closed 7 months ago
1
add new workflow scaffold_and_refine_multitaxa

#506 dpark01 closed 7 months ago
0
mass update of upstream docker tags

#505 dpark01 closed 8 months ago
0
add reconstructR workflow

#504 dpark01 closed 9 months ago
0