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.

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

Update ci.yml #92

Open
wants to merge 3 commits into
base: dev
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ jobs:
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

Expand Down
1 change: 1 addition & 0 deletions lsf_error.622473.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Nextflow 24.10.2 is available - Please consider updating your version to it
1 change: 1 addition & 0 deletions lsf_error.623156.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Nextflow 24.10.2 is available - Please consider updating your version to it
1 change: 1 addition & 0 deletions lsf_error.623571.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Nextflow 24.10.2 is available - Please consider updating your version to it
1,080 changes: 1,080 additions & 0 deletions lsf_output.622473.txt

Large diffs are not rendered by default.

645 changes: 645 additions & 0 deletions lsf_output.623156.txt

Large diffs are not rendered by default.

3,067 changes: 3,067 additions & 0 deletions lsf_output.623571.txt

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion subworkflows/local/align_pacbio.nf
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ workflow ALIGN_PACBIO {


// Align Fastq to Genome
MINIMAP2_ALIGN ( FILTER_PACBIO.out.fastq, fasta, true, false, false )
MINIMAP2_ALIGN ( FILTER_PACBIO.out.fastq, fasta, true, false, false, false )
ch_versions = ch_versions.mix ( MINIMAP2_ALIGN.out.versions.first() )


Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/filter_pacbio.nf
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ workflow FILTER_PACBIO {


// Collate BAM file to create interleaved FASTA
SAMTOOLS_COLLATE ( SAMTOOLS_CONVERT.out.bam, [] )
SAMTOOLS_COLLATE ( SAMTOOLS_CONVERT.out.bam, [[],[]] )
ch_versions = ch_versions.mix ( SAMTOOLS_COLLATE.out.versions.first() )


Expand Down
Loading