Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: peterk87/nf-flu
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: 2.0.1
Choose a base ref
...
head repository: peterk87/nf-flu
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: master
Choose a head ref
4 contributors

Commits on Apr 8, 2022

  1. workflow for nanopore data

    @nhhaidee
    nhhaidee committed Apr 8, 2022
    Copy the full SHA
    5245d2a View commit details

  2. update bcf

    @nhhaidee
    nhhaidee committed Apr 8, 2022
    Copy the full SHA
    5173eb2 View commit details

Commits on Apr 10, 2022

  1. fixes for coverage plot

    @nhhaidee
    nhhaidee committed Apr 10, 2022
    Copy the full SHA
    1b89e19 View commit details

Commits on Apr 12, 2022

  1. update worflow P2

    @nhhaidee
    nhhaidee committed Apr 12, 2022
    Copy the full SHA
    f898733 View commit details

Commits on Apr 13, 2022

  1. update workflow P3

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    d2bfae9 View commit details

  2. update workflow P4

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    ae8176e View commit details

  3. update command for nanopore workflow in README

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    f65bfa9 View commit details

  4. update nextflow_schema.json

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    acc2ac6 View commit details

  5. update missing params

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    3028ba3 View commit details

  6. enhance cat_fastq process

    @nhhaidee
    nhhaidee committed Apr 13, 2022
    Copy the full SHA
    29e0677 View commit details

Commits on Apr 14, 2022

  1. get software version and fix typos

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    551f667 View commit details

  2. output log for some processes and change process priority

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    df45ff8 View commit details

  3. remove unused params

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    4d0fab0 View commit details

  4. update medaka process

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    cbbef4b View commit details

  5. provide low_coverage params to coverage plot

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    c03d39d View commit details

  6. create illumina and nanopore config file

    @nhhaidee
    nhhaidee committed Apr 14, 2022
    Copy the full SHA
    f09a8a3 View commit details

Commits on Apr 15, 2022

  1. update names for consensus fasta file

    @nhhaidee
    nhhaidee committed Apr 15, 2022
    Copy the full SHA
    d600cac View commit details

  2. use latest mosdepth 0.3.3

    @nhhaidee
    nhhaidee committed Apr 15, 2022
    Copy the full SHA
    f9772ed View commit details

  3. add header for csv file of pulling top references

    @nhhaidee
    nhhaidee committed Apr 15, 2022
    Copy the full SHA
    c51ba70 View commit details

  4. publish barcode count sheet

    @nhhaidee
    nhhaidee committed Apr 15, 2022
    Copy the full SHA
    08e5ddc View commit details

  5. publish barcode count sheet into seprate folder

    @nhhaidee
    nhhaidee committed Apr 15, 2022
    Copy the full SHA
    d25de35 View commit details

Commits on Apr 17, 2022

  1. fix file naming issue and change samplesheet format

    @nhhaidee
    nhhaidee committed Apr 17, 2022
    Copy the full SHA
    bbda65d View commit details

Commits on Apr 18, 2022

  1. add option ref_sequences

    @nhhaidee
    nhhaidee committed Apr 18, 2022
    Copy the full SHA
    dc2f5e4 View commit details

Commits on Apr 20, 2022

  1. add CI test P1

    @nhhaidee
    nhhaidee committed Apr 20, 2022
    Copy the full SHA
    98472ed View commit details

  2. fix cov plot in case no mapping, produce empty plot

    @nhhaidee
    nhhaidee committed Apr 20, 2022
    Copy the full SHA
    02abdce View commit details

Commits on Apr 21, 2022

  1. variant calling using Clair3

    @nhhaidee
    nhhaidee committed Apr 21, 2022
    Copy the full SHA
    3725958 View commit details

Commits on Apr 22, 2022

  1. add skip_clair3

    @nhhaidee
    nhhaidee committed Apr 22, 2022
    Copy the full SHA
    d8a3a7f View commit details

Commits on Apr 25, 2022

  1. add ref_db option

    @nhhaidee
    nhhaidee committed Apr 25, 2022
    Copy the full SHA
    88a97a4 View commit details

  2. add max_top_blastn option

    @nhhaidee
    nhhaidee committed Apr 25, 2022
    Copy the full SHA
    9470130 View commit details

  3. fix duplicate index

    @nhhaidee
    nhhaidee committed Apr 25, 2022
    Copy the full SHA
    e7c90fd View commit details

  4. rename some processes

    @nhhaidee
    nhhaidee committed Apr 25, 2022
    Copy the full SHA
    8cdd510 View commit details

Commits on Apr 26, 2022

  1. fix illuminia CI test

    @nhhaidee
    nhhaidee committed Apr 26, 2022
    Copy the full SHA
    5abced2 View commit details

Commits on Apr 27, 2022

  1. remove unnecessary processes

    @nhhaidee
    nhhaidee committed Apr 27, 2022
    Copy the full SHA
    fef0fec View commit details

Commits on Apr 28, 2022

  1. add process to report mismatch of blastn results

    @nhhaidee
    nhhaidee committed Apr 28, 2022
    Copy the full SHA
    e9e0b96 View commit details

  2. add sum of mismatch

    @nhhaidee
    nhhaidee committed Apr 28, 2022
    Copy the full SHA
    4bb05fb View commit details

  3. fix typos

    @nhhaidee
    nhhaidee committed Apr 28, 2022
    Copy the full SHA
    4243099 View commit details

  4. fix typo P2

    @nhhaidee
    nhhaidee committed Apr 28, 2022
    Copy the full SHA
    dff3f33 View commit details

Commits on Apr 29, 2022

  1. update usage/doc

    @nhhaidee
    nhhaidee committed Apr 29, 2022
    Copy the full SHA
    e791255 View commit details

  2. update usage/doc P2

    @nhhaidee
    nhhaidee committed Apr 29, 2022
    Copy the full SHA
    31cb803 View commit details

Commits on May 2, 2022

  1. update clair3 container

    @nhhaidee
    nhhaidee committed May 2, 2022
    Copy the full SHA
    15a0494 View commit details

Commits on May 5, 2022

  1. updates for containers for clair3, bcftools

    @nhhaidee
    nhhaidee committed May 5, 2022
    Copy the full SHA
    17ad81c View commit details

  2. provide option variant_caller

    @nhhaidee
    nhhaidee committed May 5, 2022
    Copy the full SHA
    d283fb1 View commit details

  3. set clair3 by default

    @nhhaidee
    nhhaidee committed May 5, 2022
    Copy the full SHA
    c4b6df6 View commit details

Commits on May 6, 2022

  1. no_phasing_for_fa

    @nhhaidee
    nhhaidee committed May 6, 2022
    Copy the full SHA
    53dbe4e View commit details

  2. no_phasing_for_fa is false

    @nhhaidee
    nhhaidee committed May 6, 2022
    Copy the full SHA
    8d93b3b View commit details

Commits on May 9, 2022

  1. update singularity in config file

    @nhhaidee
    nhhaidee committed May 9, 2022
    Copy the full SHA
    468505e View commit details

Commits on May 10, 2022

  1. update IRMA container

    @nhhaidee
    nhhaidee committed May 10, 2022
    Copy the full SHA
    2dcb2ee View commit details

  2. use mamba to create conda env

    @nhhaidee
    nhhaidee committed May 10, 2022
    Copy the full SHA
    49a64cd View commit details

  3. update docs and remove useMamba

    @nhhaidee
    nhhaidee committed May 10, 2022
    Copy the full SHA
    327c70b View commit details

Commits on May 11, 2022

  1. update output.md

    @nhhaidee
    nhhaidee committed May 11, 2022
    Copy the full SHA
    6e52f59 View commit details
Loading