Code

streamline NCBI submissions#191

Code

Merged

dpark01 merged 55 commits intomasterbroadinstitute/viral-pipelines:masterfrom dp-genbankbroadinstitute/viral-pipelines:dp-genbankCopy head branch name to clipboardJan 12, 2021

+1,255-115

Commits

Commits on Jan 6, 2021

• bump viral-phylo and add package_genbank_ftp_submission task (not used in workflow yet)

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  committed
  45c34e1

• bump viral-phylo

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  45135e6

• bump requirements for viral-phylo

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  2428edc

• add vadr task, add sarscov2_genbank workflow

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  ca53a37

• strip trailing . from basename

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  d6d995d

• fix wdl variable replacement for spuid

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  fb4795f

• add rename_fasta task

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  2af04ed

• tweaks to sarscov2_genbank

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  506ffef

Commits on Jan 7, 2021

• implement table lookup

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  bda4466

• strip .fasta from filename in id lookup

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  b3e34c2

• optimize table lookup; bugfix rename_fasta

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  f8e123e

• oops, new name isnt always filename sanitary

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  1fd33c0

• odd, this didnt go through

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  9062be8

• Cromwell/womtool/Terra require us to split this basename call out for some reason

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  f1f673e

• fix indent

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  15df05f

• oops, replace input file with WDL input file

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  7c62da1

• bump nextclade and pangolin docker images

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  08bae4c

• bugfix

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  5d9012e

• simplify

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  ca4b227

• count lines in a more cross-platform way

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  e58ad1d

• fix line count

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  e811cd3

Commits on Jan 8, 2021

• bugfix assembly_bases

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  5b53955

• bump viral-phylo docker image to update the date string we get for genbanks source modifier table

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  cb66614

• update vadr docker image

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  1ac38b1

• update vadr_opts

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  b1a1cf5

Commits on Jan 9, 2021

• backport mem increase from branch mem_inc_sc

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  08a4fd3

• add multi-metadata-tsv merge to subsample_by_metadata_with_focal

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  08b7b04

Commits on Jan 10, 2021

• mafft_and_snp tolerates compressed fasta inputs, add derived_cols to post metadata merge in subsample_by_metadata_with_focal

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  1cd3b92

• convert augur_from_assemblies into an uberworkflow of three subworkflows

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  e2863d0

• update some refine_tree defaults to match nextstrain current best practice

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  38c9809

• finish out augur_from_assemblies rewrite and fix unit test spec

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  8bc7b29

• bind auspice_config and run_iqtree

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  1b14d12

• convert augur_from_assemblies away from subworkflows to expose task-level options properly

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  8191c5d

• bugfix

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  80199a9

• decompress to temp file

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  d78ed5f

• more mafft ram default

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  c593e5e

• remove all subworkflows and see if that fixes things

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  a5a5e1d

• add demux_deplete workflow

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  1c57025

• remove gzipped msa from augur_from_assemblies for now

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  59b19a1

Commits on Jan 11, 2021

• implement length filter

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  604add5

• add required input param to test

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  230399a

• performance increase

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  e4686b6

• increase default mafft mem size.. for some reason

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  6de232d

• first fully working demux_deplete workflow

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  84d5167

Commits on Jan 12, 2021

• obo bugfix

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  737c68d

• bump viral-core

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  6903e6c

• initial stab at full workflow

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  62034b2

• change debug output for sra_meta_prep

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  e80f621

• fix up illumina_full

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  f178755

• bam filenames were sanitized by illumina.py

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  bb2085f

• oops, sanitized the wrong field

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  9d6eb39

• restore old code

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  6da2d05

• wrong sanitizing function

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  5cb8926

• fix to conform to sra meta spec

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  6bace96

• add assembly=unaligned for sra meta

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  1c0c944