Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Dev > Master for 3.0 release #534

Merged
merged 209 commits into from
Dec 15, 2020
Merged

Dev > Master for 3.0 release #534

merged 209 commits into from
Dec 15, 2020

Commits on Nov 13, 2020

  1. Bump version to 2.1dev

    @drpatelh
    drpatelh committed Nov 13, 2020
    Configuration menu
    Copy the full SHA
    bb9b4fe View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @drpatelh
    drpatelh committed Nov 13, 2020
    Configuration menu
    Copy the full SHA
    8dcf148 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #497 from drpatelh/dsl2 

    Bump-versions to 2.1dev
    @drpatelh
    drpatelh authored Nov 13, 2020
    Configuration menu
    Copy the full SHA
    39d1a65 View commit details
    Browse the repository at this point in the history

Commits on Nov 19, 2020

  1. Template update for nf-core/tools version 1.12

    @nf-core-bot
    nf-core-bot committed Nov 19, 2020
    Configuration menu
    Copy the full SHA
    82a71c9 View commit details
    Browse the repository at this point in the history

  2. Initialise args for umitools extract

    @drpatelh
    drpatelh committed Nov 19, 2020
    Configuration menu
    Copy the full SHA
    906d610 View commit details
    Browse the repository at this point in the history

Commits on Nov 23, 2020

  1. Fix merge conflicts

    @drpatelh
    drpatelh committed Nov 23, 2020
    Configuration menu
    Copy the full SHA
    a7a97b3 View commit details
    Browse the repository at this point in the history

  2. Replace baseDir with projectDir

    @drpatelh
    drpatelh committed Nov 23, 2020
    Configuration menu
    Copy the full SHA
    66740fb View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' of https://github.com/nf-core/rnaseq into dsl2

    @drpatelh
    drpatelh committed Nov 23, 2020
    Configuration menu
    Copy the full SHA
    d563fa3 View commit details
    Browse the repository at this point in the history

  4. Change genome wording

    @drpatelh
    drpatelh committed Nov 23, 2020
    Configuration menu
    Copy the full SHA
    a84b4c8 View commit details
    Browse the repository at this point in the history

  5. Merge pull request #502 from drpatelh/dsl2 

    Initialise args for umitools extract
    @drpatelh
    drpatelh authored Nov 23, 2020
    Configuration menu
    Copy the full SHA
    3d254ee View commit details
    Browse the repository at this point in the history

Commits on Nov 24, 2020

  1. Update CHANGELOG

    @drpatelh
    drpatelh committed Nov 24, 2020
    Configuration menu
    Copy the full SHA
    f94e393 View commit details
    Browse the repository at this point in the history

  2. Fix AWS batch assert issues

    @drpatelh
    drpatelh committed Nov 24, 2020
    Configuration menu
    Copy the full SHA
    3637e74 View commit details
    Browse the repository at this point in the history

  3. Invert logic

    @drpatelh
    drpatelh committed Nov 24, 2020
    Configuration menu
    Copy the full SHA
    0c372f7 View commit details
    Browse the repository at this point in the history

  4. Remove crick profile test

    @drpatelh
    drpatelh committed Nov 24, 2020
    Configuration menu
    Copy the full SHA
    2ca2d16 View commit details
    Browse the repository at this point in the history

  5. Both need to be true

    @drpatelh
    drpatelh committed Nov 24, 2020
    Configuration menu
    Copy the full SHA
    b236d2e View commit details
    Browse the repository at this point in the history

  6. Merge pull request #510 from drpatelh/dsl2 

    Fix awsbatch assert issue
    @drpatelh
    drpatelh authored Nov 24, 2020
    Configuration menu
    Copy the full SHA
    9b54e51 View commit details
    Browse the repository at this point in the history

Commits on Nov 30, 2020

  1. Add STAR parameter when building small indices

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    56496c0 View commit details
    Browse the repository at this point in the history

  2. Adjust spacing

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    38640e2 View commit details
    Browse the repository at this point in the history

  3. Adjust spacing

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    d2cf076 View commit details
    Browse the repository at this point in the history

  4. Use STAR to build initial index for RSEM

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    ad87ea7 View commit details
    Browse the repository at this point in the history

  5. Update CHANGELOG

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    0e483db View commit details
    Browse the repository at this point in the history

  6. Install via nf-core modules

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    e2afdfa View commit details
    Browse the repository at this point in the history

  7. fastq not bam

    @drpatelh
    drpatelh committed Nov 30, 2020
    Configuration menu
    Copy the full SHA
    91a0d10 View commit details
    Browse the repository at this point in the history

Commits on Dec 1, 2020

  1. Allow for dots in sample names @ChristopherBarrington

    @drpatelh
    drpatelh committed Dec 1, 2020
    Configuration menu
    Copy the full SHA
    edc5df7 View commit details
    Browse the repository at this point in the history

  2. Remove specifying --outdir twice

    @drpatelh
    drpatelh committed Dec 1, 2020
    Configuration menu
    Copy the full SHA
    01d0fc6 View commit details
    Browse the repository at this point in the history

  3. Add a note about running separate arms of pipeline

    @drpatelh
    drpatelh committed Dec 1, 2020
    Configuration menu
    Copy the full SHA
    76bea0c View commit details
    Browse the repository at this point in the history

  4. Indent section

    @drpatelh
    drpatelh committed Dec 1, 2020
    Configuration menu
    Copy the full SHA
    641dfbc View commit details
    Browse the repository at this point in the history

  5. Merge pull request #512 from drpatelh/dsl2 

    Use STAR to build initial index for RSEM - Fixes #511
    @drpatelh
    drpatelh authored Dec 1, 2020
    Configuration menu
    Copy the full SHA
    5288244 View commit details
    Browse the repository at this point in the history

Commits on Dec 2, 2020

  1. Update salmon tximport 

    thanks to @tamuanand
issue #499
    Lorena Pantano committed Dec 2, 2020
    Configuration menu
    Copy the full SHA
    1ca2fb1 View commit details
    Browse the repository at this point in the history

Commits on Dec 3, 2020

  1. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    7005210 View commit details
    Browse the repository at this point in the history

  2. Add conda.cachedir note

    @drpatelh
    drpatelh committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    2268749 View commit details
    Browse the repository at this point in the history

  3. Fix InvocationTargetException by not using checkIfExists

    @drpatelh
    drpatelh committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    cd8aacc View commit details
    Browse the repository at this point in the history

  4. Merge pull request #522 from drpatelh/fastq_input 

    Fix #516 InvocationTargetException by not using checkIfExists
    @drpatelh
    drpatelh authored Dec 3, 2020
    Configuration menu
    Copy the full SHA
    f0fda1f View commit details
    Browse the repository at this point in the history

  5. Template update for nf-core/tools version 1.12.1

    @nf-core-bot
    nf-core-bot committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    f690b89 View commit details
    Browse the repository at this point in the history

  6. fix naming for variables

    Lorena Pantano committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    9537632 View commit details
    Browse the repository at this point in the history

  7. Fix typo on function names and files output

    Lorena Pantano committed Dec 3, 2020
    Configuration menu
    Copy the full SHA
    ca9063a View commit details
    Browse the repository at this point in the history

Commits on Dec 4, 2020

  1. Merge pull request #519 from nf-core/patch-499 

    Update salmon tximport
    @drpatelh
    drpatelh authored Dec 4, 2020
    Configuration menu
    Copy the full SHA
    dee07c2 View commit details
    Browse the repository at this point in the history

  2. Fix merge conflicts

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    863f68b View commit details
    Browse the repository at this point in the history

  3. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    a9e769f View commit details
    Browse the repository at this point in the history

  4. Add references

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    9113360 View commit details
    Browse the repository at this point in the history

  5. Replace featureCounts with Salmon

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    b99b488 View commit details
    Browse the repository at this point in the history

  6. Change emit names

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    c58cef2 View commit details
    Browse the repository at this point in the history

  7. Adjust spacing

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    4f84ae9 View commit details
    Browse the repository at this point in the history

  8. Adjust spacing

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    d93d7a3 View commit details
    Browse the repository at this point in the history

  9. Use length scaled counts for DESeq2

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    6f95e3e View commit details
    Browse the repository at this point in the history

  10. Build index using decoy sequences

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    4561818 View commit details
    Browse the repository at this point in the history

  11. Add line break

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    c411e17 View commit details
    Browse the repository at this point in the history

  12. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    19bd2a0 View commit details
    Browse the repository at this point in the history

  13. Pass genome fasta to indexing

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    7226aef View commit details
    Browse the repository at this point in the history

  14. Prep transcripts fasta too

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    69e4cbc View commit details
    Browse the repository at this point in the history

  15. Prep transcripts fasta too

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    5b7a0e4 View commit details
    Browse the repository at this point in the history

  16. Remove featureCounts settings

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    24f850b View commit details
    Browse the repository at this point in the history

  17. Remove featureCounts files

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    bda44c6 View commit details
    Browse the repository at this point in the history

  18. Minor updates

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    cdcfc96 View commit details
    Browse the repository at this point in the history

  19. Add skip_alignment_quant parameter

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    25e40f4 View commit details
    Browse the repository at this point in the history

  20. Minor updates

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    51e88f6 View commit details
    Browse the repository at this point in the history

  21. Provide BAM as input too

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    b86bd5d View commit details
    Browse the repository at this point in the history

  22. Remove featurecounts merge module

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    52c0fc3 View commit details
    Browse the repository at this point in the history

  23. Change folder name

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    d519f86 View commit details
    Browse the repository at this point in the history

  24. Change default params

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    fbe1556 View commit details
    Browse the repository at this point in the history

  25. Remove featurecounts plot

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    d94bd58 View commit details
    Browse the repository at this point in the history

  26. Update output docs

    @drpatelh
    drpatelh committed Dec 4, 2020
    Configuration menu
    Copy the full SHA
    eede4da View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2020

  1. Add function to check if params.genomes exists

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    d681bed View commit details
    Browse the repository at this point in the history

  2. Initialise reference parameters in main script

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    3d07775 View commit details
    Browse the repository at this point in the history

  3. Accommodate reference paramters

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    27cc880 View commit details
    Browse the repository at this point in the history

  4. Move reference option initialisation

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    08f93ae View commit details
    Browse the repository at this point in the history

  5. Initialise params.genomes

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    f7ef798 View commit details
    Browse the repository at this point in the history

  6. Minor updates

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    1ca342c View commit details
    Browse the repository at this point in the history

  7. Update main script

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    c545044 View commit details
    Browse the repository at this point in the history

  8. Move igenomes.config code up a bit

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    8fc443b View commit details
    Browse the repository at this point in the history

  9. Minor update

    @drpatelh
    drpatelh committed Dec 7, 2020
    Configuration menu
    Copy the full SHA
    bc4284f View commit details
    Browse the repository at this point in the history

Commits on Dec 8, 2020

  1. Strip out index creation to separte workflow

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    82c0870 View commit details
    Browse the repository at this point in the history

  2. Move star index creation to prepare_genome workflow

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    8e11977 View commit details
    Browse the repository at this point in the history

  3. Fix spacing

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    8435f54 View commit details
    Browse the repository at this point in the history

  4. Move indexing to separate sub-workflow

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    bf4ee87 View commit details
    Browse the repository at this point in the history

  5. Add in HISAT2 indexing process

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    ed66620 View commit details
    Browse the repository at this point in the history

  6. Add version commands

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    e1b923d View commit details
    Browse the repository at this point in the history

  7. Move RSEM index creation to separate process

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    4cfdf3f View commit details
    Browse the repository at this point in the history

  8. Add RSEM indexing processes

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    eb1aa41 View commit details
    Browse the repository at this point in the history

  9. Minor tweaks

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    9120bbd View commit details
    Browse the repository at this point in the history

  10. Remove indexing steps

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    b81ff59 View commit details
    Browse the repository at this point in the history

  11. Add in Salmon indexing

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    d0dbff7 View commit details
    Browse the repository at this point in the history

  12. Alter sub-workflow options

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    911bc66 View commit details
    Browse the repository at this point in the history

  13. Final amendments

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    ebd3a34 View commit details
    Browse the repository at this point in the history

  14. Minor updates

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    0ef6cd2 View commit details
    Browse the repository at this point in the history

  15. Only create indices when required

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    14eb4b2 View commit details
    Browse the repository at this point in the history

  16. Only create indices when required

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    e3e0565 View commit details
    Browse the repository at this point in the history

  17. Adjust spacing

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    1997bc1 View commit details
    Browse the repository at this point in the history

  18. Add in STAR RSEM

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    d56556b View commit details
    Browse the repository at this point in the history

  19. Rename index channel

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    88ba3d2 View commit details
    Browse the repository at this point in the history

  20. Add in processes

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    de52919 View commit details
    Browse the repository at this point in the history

  21. Add options for STAR Salmon processes

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    0103e00 View commit details
    Browse the repository at this point in the history

  22. Remove skip_alignment_quant parameter

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    10819e4 View commit details
    Browse the repository at this point in the history

  23. Change star to star_salmon

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    ce9b4e5 View commit details
    Browse the repository at this point in the history

  24. Change star to star_salmon

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    a0f1648 View commit details
    Browse the repository at this point in the history

  25. Add explicit tximport options

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    917fd85 View commit details
    Browse the repository at this point in the history

  26. Get STAR Salmon working

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    7624f97 View commit details
    Browse the repository at this point in the history

  27. Change variable names

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    55d9cfd View commit details
    Browse the repository at this point in the history

  28. Add all processes back in. Wooooohoooooo

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    eb7eb4c View commit details
    Browse the repository at this point in the history

  29. Change standard transgene fields

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    11c8243 View commit details
    Browse the repository at this point in the history

  30. Change params from fc_ to gtf_

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    51a0947 View commit details
    Browse the repository at this point in the history

  31. Update schema

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    55345a6 View commit details
    Browse the repository at this point in the history

  32. Change params from fc_ to gtf_

    @drpatelh
    drpatelh committed Dec 8, 2020
    Configuration menu
    Copy the full SHA
    34c1eba View commit details
    Browse the repository at this point in the history

Commits on Dec 9, 2020

  1. Change parameter names

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    b39b390 View commit details
    Browse the repository at this point in the history

  2. Change fc_ to gtf_

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    8a9e2e8 View commit details
    Browse the repository at this point in the history

  3. Update output docs

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    6d2a126 View commit details
    Browse the repository at this point in the history

  4. Update usage docs

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    2f009d9 View commit details
    Browse the repository at this point in the history

  5. Update --aligner star_salmon

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    0c1a1dc View commit details
    Browse the repository at this point in the history

  6. Get channel order right

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    333f439 View commit details
    Browse the repository at this point in the history

  7. Minor tweaks

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    b85ff88 View commit details
    Browse the repository at this point in the history

  8. Add note to README about HISAT2

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    07d6cdd View commit details
    Browse the repository at this point in the history

  9. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    9327bdf View commit details
    Browse the repository at this point in the history

  10. Add description of no quant with HISAT2

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    4d6c784 View commit details
    Browse the repository at this point in the history

  11. Add note about differing STAR indices versions

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    58b702f View commit details
    Browse the repository at this point in the history

  12. Add spacing

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    c32c8e9 View commit details
    Browse the repository at this point in the history

  13. Fix markdownlint

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    69676cb View commit details
    Browse the repository at this point in the history

  14. Move chrom sizes file to prep genome sub-workflow

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    1d21ac5 View commit details
    Browse the repository at this point in the history

  15. Add test for creation of transcripts.fasta

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    9d8dbb8 View commit details
    Browse the repository at this point in the history

  16. Move chrom sizes file to prep genome sub-workflow

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    8379a9d View commit details
    Browse the repository at this point in the history

  17. Remove featureCounts settings

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    5ee3748 View commit details
    Browse the repository at this point in the history

  18. Fix tyop

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    0b95e86 View commit details
    Browse the repository at this point in the history

  19. Fix DESEQ2 QC labels

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    23a0b32 View commit details
    Browse the repository at this point in the history

  20. Fix tyop everywhere yo

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    4d93149 View commit details
    Browse the repository at this point in the history

  21. Minor updates

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    7a0f923 View commit details
    Browse the repository at this point in the history

  22. Adjust spacing

    @drpatelh
    drpatelh committed Dec 9, 2020
    Configuration menu
    Copy the full SHA
    565daaf View commit details
    Browse the repository at this point in the history

Commits on Dec 10, 2020

  1. Use params directly in sub-workflow

    @drpatelh
    drpatelh committed Dec 10, 2020
    Configuration menu
    Copy the full SHA
    c79f441 View commit details
    Browse the repository at this point in the history

  2. Delete explicit params listing

    @drpatelh
    drpatelh committed Dec 10, 2020
    Configuration menu
    Copy the full SHA
    370a83b View commit details
    Browse the repository at this point in the history

  3. Remove commented section

    @drpatelh
    drpatelh committed Dec 10, 2020
    Configuration menu
    Copy the full SHA
    43fabdd View commit details
    Browse the repository at this point in the history

  4. Change variable name for consistency

    @drpatelh
    drpatelh committed Dec 10, 2020
    Configuration menu
    Copy the full SHA
    e3c0c91 View commit details
    Browse the repository at this point in the history

Commits on Dec 11, 2020

  1. Re-write STAR Salmon section

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    9a0268a View commit details
    Browse the repository at this point in the history

  2. Update Salmon section in output docs

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    5de060a View commit details
    Browse the repository at this point in the history

  3. Fix markdownlint

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    db5aeec View commit details
    Browse the repository at this point in the history

  4. Add Singularity containers back in

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    ab93328 View commit details
    Browse the repository at this point in the history

  5. Use biocontainer

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    205dc8a View commit details
    Browse the repository at this point in the history

  6. Add singularity_pull_docker_container to Schema

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    3801597 View commit details
    Browse the repository at this point in the history

  7. Use ch_gff_version for consistency

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    addabcf View commit details
    Browse the repository at this point in the history

  8. Fix gentrome variable

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    f3d7667 View commit details
    Browse the repository at this point in the history

  9. Bump Nextflow to 20.11.0-edge

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    f06248e View commit details
    Browse the repository at this point in the history

  10. Merge pull request #526 from drpatelh/salmon 

    Replace featureCounts with Salmon quant
    @drpatelh
    drpatelh authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    69d024f View commit details
    Browse the repository at this point in the history

  11. Fix merge conflicts

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    db667cd View commit details
    Browse the repository at this point in the history

  12. Remove latest tests for latest stable NF release

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    3bf0c28 View commit details
    Browse the repository at this point in the history

  13. Add description of --singularity_pull_docker_container

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    7257eea View commit details
    Browse the repository at this point in the history

  14. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    f682754 View commit details
    Browse the repository at this point in the history

  15. Fix badge

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    9319bd0 View commit details
    Browse the repository at this point in the history

  16. Update CHANGELOG.md

    @drpatelh
    drpatelh authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    2c30f94 View commit details
    Browse the repository at this point in the history

  17. add a tip to show how we produce salmon outputs

    Lorena Pantano committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    aa2e73f View commit details
    Browse the repository at this point in the history

  18. add @mikelove recommentation

    Lorena Pantano committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    1789c8c View commit details
    Browse the repository at this point in the history

  19. Update CHANGELOG.md 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @drpatelh @ewels
    drpatelh and ewels authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    03ee83f View commit details
    Browse the repository at this point in the history

  20. Update CHANGELOG.md 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @drpatelh @ewels
    drpatelh and ewels authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    84cf839 View commit details
    Browse the repository at this point in the history

  21. Update CHANGELOG.md 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @drpatelh @ewels
    drpatelh and ewels authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    39f9388 View commit details
    Browse the repository at this point in the history

  22. Update CHANGELOG.md 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @drpatelh @ewels
    drpatelh and ewels authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    ad20b22 View commit details
    Browse the repository at this point in the history

  23. Update README.md 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @drpatelh @ewels
    drpatelh and ewels authored Dec 11, 2020
    Configuration menu
    Copy the full SHA
    38a7db0 View commit details
    Browse the repository at this point in the history

  24. Bump pipeline version to 3.0

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    f454485 View commit details
    Browse the repository at this point in the history

  25. Merge branch 'https' of https://github.com/drpatelh/rnaseq into https

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    7a8e9a2 View commit details
    Browse the repository at this point in the history

  26. Fix markdownlint

    @drpatelh
    drpatelh committed Dec 11, 2020
    Configuration menu
    Copy the full SHA
    c23872f View commit details
    Browse the repository at this point in the history

Commits on Dec 12, 2020

  1. Add in @rob-p default settings for Salmon

    @drpatelh
    drpatelh committed Dec 12, 2020
    Configuration menu
    Copy the full SHA
    58e5711 View commit details
    Browse the repository at this point in the history

  2. Remove line break

    @drpatelh
    drpatelh committed Dec 12, 2020
    Configuration menu
    Copy the full SHA
    e25e3c8 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #531 from drpatelh/https 

    Direct download of Singularity biocontainer images. Fixes #494 and #496
    @drpatelh
    drpatelh authored Dec 12, 2020
    Configuration menu
    Copy the full SHA
    2c732fa View commit details
    Browse the repository at this point in the history

Commits on Dec 13, 2020

  1. Fix #525

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    f33eb6d View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    d05d617 View commit details
    Browse the repository at this point in the history

  3. List software changes

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    dffe81e View commit details
    Browse the repository at this point in the history

  4. Update software versions

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    ef9eae6 View commit details
    Browse the repository at this point in the history

  5. Use requests container

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    2495bbc View commit details
    Browse the repository at this point in the history

  6. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 13, 2020
    Configuration menu
    Copy the full SHA
    c0250a2 View commit details
    Browse the repository at this point in the history

  7. Update docs/output.md

    @drpatelh
    drpatelh authored Dec 13, 2020
    Configuration menu
    Copy the full SHA
    e1611ef View commit details
    Browse the repository at this point in the history

Commits on Dec 14, 2020

  1. Merge pull request #532 from nf-core/patch-salmon-doc 

    add a tip to show how we produce salmon outputs
    @drpatelh
    drpatelh authored Dec 14, 2020
    Configuration menu
    Copy the full SHA
    521038c View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' of https://github.com/nf-core/rnaseq into release

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    29037fe View commit details
    Browse the repository at this point in the history

  3. Sync modules with nf-core/modules

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    3412363 View commit details
    Browse the repository at this point in the history

  4. Optional input for STAR / Salmon quant

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    69a4b07 View commit details
    Browse the repository at this point in the history

  5. Do not stage transcripts fasta for Salmon

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    13c5c0c View commit details
    Browse the repository at this point in the history

  6. Only pin DESeq2 and r-base for QC plot module

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    c2a7fff View commit details
    Browse the repository at this point in the history

  7. Add check if bioconda channels are set-up correctly

    @grst
    grst committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    72b867b View commit details
    Browse the repository at this point in the history

  8. Update changelog

    @grst
    grst committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    53cbf76 View commit details
    Browse the repository at this point in the history

  9. Fix error message

    @grst
    grst committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    2e5de19 View commit details
    Browse the repository at this point in the history

  10. Raise warning instead of hard failure. 

     * Uses `log.warn` instead of `assert` in order not to cause a hard
 failure when a problem is detected
 * Uses try/catch to handle cases where conda is not installed, or the
 `~/.condarc` file is invalid.
    @grst
    grst committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    4b0cbee View commit details
    Browse the repository at this point in the history

  11. Update DESeq2 docs

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    af322a0 View commit details
    Browse the repository at this point in the history

  12. Update lib/Checks.groovy 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @grst @drpatelh
    grst and drpatelh authored Dec 14, 2020
    Configuration menu
    Copy the full SHA
    c5aa2a9 View commit details
    Browse the repository at this point in the history

  13. Update lib/Checks.groovy 

    Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
    @grst @drpatelh
    grst and drpatelh authored Dec 14, 2020
    Configuration menu
    Copy the full SHA
    125d4ae View commit details
    Browse the repository at this point in the history

  14. Fix indent

    @grst
    grst committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    f561896 View commit details
    Browse the repository at this point in the history

  15. Update Salmon tximport docs

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    5ed68e9 View commit details
    Browse the repository at this point in the history

  16. Merge pull request #537 from grst/dev 

    Add check if bioconda channels are set-up correctly
    @drpatelh
    drpatelh authored Dec 14, 2020
    Configuration menu
    Copy the full SHA
    cd39948 View commit details
    Browse the repository at this point in the history

  17. Fix merge conflicts

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    e4a6e37 View commit details
    Browse the repository at this point in the history

  18. Minor updates to Conda check function

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    265cb59 View commit details
    Browse the repository at this point in the history

  19. Run checks after parameter summary

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    d6ad2eb View commit details
    Browse the repository at this point in the history

  20. update pubmed url schema.

    matthiasho committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    f098df8 View commit details
    Browse the repository at this point in the history

  21. Fix markdownlint

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    abb4ac3 View commit details
    Browse the repository at this point in the history

  22. Check that re-sequenced have same strandedness

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    1660cfc View commit details
    Browse the repository at this point in the history

  23. Incorporate additional link in docs suggested by @tamuanand

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    ccd21ea View commit details
    Browse the repository at this point in the history

  24. Merge pull request #538 from mashehu/dev 

    update pubmed url schema.
    @drpatelh
    drpatelh authored Dec 14, 2020
    Configuration menu
    Copy the full SHA
    cd886e4 View commit details
    Browse the repository at this point in the history

  25. Merge branch 'dev' of https://github.com/nf-core/rnaseq into release

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    f9f495c View commit details
    Browse the repository at this point in the history

  26. Use logo with white background

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    24eca89 View commit details
    Browse the repository at this point in the history

  27. Use opaque logo

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    d930c09 View commit details
    Browse the repository at this point in the history

  28. Use white background logo

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    0dbd62c View commit details
    Browse the repository at this point in the history

  29. Add options for ucsc_bedclip

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    0aecc7d View commit details
    Browse the repository at this point in the history

  30. Remove logo from main README

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    b2a75d5 View commit details
    Browse the repository at this point in the history

  31. Add UCSC_BEDCLIP module

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    9f3a116 View commit details
    Browse the repository at this point in the history

  32. Initial commit

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    aad3046 View commit details
    Browse the repository at this point in the history

  33. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 14, 2020
    Configuration menu
    Copy the full SHA
    f72f40a View commit details
    Browse the repository at this point in the history

Commits on Dec 15, 2020

  1. Add -E flag to gffread

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    e6a2d6c View commit details
    Browse the repository at this point in the history

  2. Make star_rsem default route for test_full

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    8a9495e View commit details
    Browse the repository at this point in the history

  3. Remove ReadCube link

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    60aab69 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #535 from drpatelh/release 

    Final pre-release updates
    @drpatelh
    drpatelh authored Dec 15, 2020
    Configuration menu
    Copy the full SHA
    6aaaa65 View commit details
    Browse the repository at this point in the history

  5. Make transcripts.fa from rsem-prepare-reference not gffread

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    09c9ac1 View commit details
    Browse the repository at this point in the history

  6. Add output channel for transcripts fasta

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    7178ddc View commit details
    Browse the repository at this point in the history

  7. Use default --aligner with test_full

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    66ba73b View commit details
    Browse the repository at this point in the history

  8. Update CHANGELOG

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    c0c82bd View commit details
    Browse the repository at this point in the history

  9. GFFREAD not GFFREAD_GFF

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    4188587 View commit details
    Browse the repository at this point in the history

  10. Remove redundant module

    @drpatelh
    drpatelh committed Dec 15, 2020
    Configuration menu
    Copy the full SHA
    a085bdd View commit details
    Browse the repository at this point in the history

  11. Merge pull request #539 from drpatelh/release 

    Use rsem-prepare-reference and not gffread to create transcripts fasta
    @drpatelh
    drpatelh authored Dec 15, 2020
    Configuration menu
    Copy the full SHA
    f05e2a2 View commit details
    Browse the repository at this point in the history