From 86f98f4d9b910c37059fb945c2a5a9a43e2aa5db Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:05:42 -0400 Subject: [PATCH 1/7] fix: increased pipeline walltime --- assets/slurm_header_biowulf.sh | 2 +- assets/slurm_header_frce.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/slurm_header_biowulf.sh b/assets/slurm_header_biowulf.sh index ce79e61..e40c800 100644 --- a/assets/slurm_header_biowulf.sh +++ b/assets/slurm_header_biowulf.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash #SBATCH --cpus-per-task=1 #SBATCH --mem=1g -#SBATCH --time=1-00:00:00 +#SBATCH --time=100:00:00 #SBATCH --parsable #SBATCH -J "LOGAN" #SBATCH --mail-type=BEGIN,END,FAIL diff --git a/assets/slurm_header_frce.sh b/assets/slurm_header_frce.sh index 957972a..a55b94b 100644 --- a/assets/slurm_header_frce.sh +++ b/assets/slurm_header_frce.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash #SBATCH --cpus-per-task=1 #SBATCH --mem=1g -#SBATCH --time=1-00:00:00 +#SBATCH --time=100:00:00 #SBATCH --parsable #SBATCH -J "LOGAN" #SBATCH --mail-type=BEGIN,END,FAIL From b02cee9dbf5ab3d145f7bd950a0515eee9c553c4 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:06:51 -0400 Subject: [PATCH 2/7] fix: removed gs bind paths from biowulf config --- conf/biowulf.config | 1 - main.nf | 0 2 files changed, 1 deletion(-) mode change 100644 => 100755 main.nf diff --git a/conf/biowulf.config b/conf/biowulf.config index 97c5c68..2d501f8 100644 --- a/conf/biowulf.config +++ b/conf/biowulf.config @@ -22,7 +22,6 @@ singularity { autoMounts = true cacheDir = "/data/CCBR_Pipeliner/SIFS" envWhitelist = 'https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH' - runOptions = '-B /gs10,/gs11,/gs12,/spin1,/data/CCBR_Pipeliner/,/vf/users,/gpfs,/fdb' } env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFS" diff --git a/main.nf b/main.nf old mode 100644 new mode 100755 From 4dc4cda1427821d9c8fc6d7e1e08b25f836da1c4 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:07:16 -0400 Subject: [PATCH 3/7] docs: updated LOGAN documentation --- README.md | 98 ++++++++++++++++++++++++++++++++++++++------------- docs/index.md | 2 +- 2 files changed, 75 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index e489fae..807de47 100644 --- a/README.md +++ b/README.md @@ -27,21 +27,24 @@ Original pipelining and code forked from the CCBR Exome-seek Pipeline [Exome-see **Requires:** `singularity>=3.5` `nextflow>=22.10.2` -[singularity](https://singularity.lbl.gov/all-releases) must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step relies on versioned images from [DockerHub](https://hub.docker.com/orgs/nciccbr/repositories). Nextflow uses singularity to pull these images onto the local filesystem prior to job execution, and as so, nextflow and singularity are the only two dependencies. +[singularity](https://singularity.lbl.gov/all-releases) must be installed on the target system. Nextflow orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step relies on versioned images from [DockerHub](https://hub.docker.com/orgs/nciccbr/repositories). Nextflow uses singularity to pull these images onto the local filesystem prior to job execution, and as so, nextflow and singularity are the only two dependencies. -## Setup +## Set up -LOGAN can be used with the Nextflow pipelining software in -Please clone this repository to your local filesystem using the following command on Biowulf: +LOGAN is installed on the [Biowulf HPC](#biowulf). +For installation in other execution environments, refer to the [docs](https://ccbr.github.io/LOGAN/). -```bash +### Biowulf + +LOGAN is available on [Biowulf](https://hpc.nih.gov/) in the `ccbrpipeliner` module. +You'll first need to start an interactive session, then load the module: + +```sh # start an interactive node sinteractive --mem=2g --cpus-per-task=2 --gres=lscratch:200 -git clone https://github.com/CCBR/LOGAN -module load nextflow -##Example run -nextflow run LOGAN/main.nf -profile ci_stub -preview +# load the ccbrpipeliner module +module load ccbrpipeliner ``` ## Usage @@ -65,8 +68,10 @@ LOGAN supports inputs of either Example ```bash -c130863309_TUMOR /data/nousomedr/c130863309_TUMOR.R1_001.fastq.gz /data/nousomedr/c130863309_TUMOR.R2_001.fastq.gz -c130889189_PBMC /data/nousomedr/c130889189_PBMC.R1_001.fastq.gz /data/nousomedr/c130889189_PBMC.R2_001.fastq.gz +Sample1_TUMOR /path/to/the/fastq/folder/Sample1_TUMOR.R1.fq.gz /path/to/the/fastq/folder/Sample1_TUMOR.R2.fq.gz +Sample1_NORMAL /path/to/the/fastq/folder/Sample1_NORMAL.R1.fq.gz /path/to/the/fastq/folder/Sample1_NORMAL.R2.fq.gz +Sample2_TUMOR /path/to/the/fastq/folder/Sample2_TUMOR.R1.fq.gz /path/to/the/fastq/folder/Sample2_TUMOR.R2.fq.gz +Sample2_NORMAL /path/to/the/fastq/folder/Sample2_NORMAL.R1.fq.gz /path/to/the/fastq/folder/Sample2_NORMAL.R2.fq.gz ``` `--bam_file_input` - A headerless tab delimited sheet that has the sample name, bam, and bam index (bai) file locations @@ -74,8 +79,8 @@ c130889189_PBMC /data/nousomedr/c130889189_PBMC.R1_001.fastq.gz /data/nousomed Example ```bash -c130863309_TUMOR /data/nousomedr/c130863309_TUMOR.bam /data/nousomedr/c130863309_TUMOR.bam.bai -c130889189_PBMC /data/nousomedr/c130889189_PBMC.bam /data/nousomedr/c130889189_PBMC.bam.bai +Sample1_TUMOR /path/to/the/BAM/folder/Sample1_TUMOR.bam /path/to/the/BAM/folder/Sample1_TUMOR.bam.bai +Sample1_NORMAL /path/to/the/BAM/folder/Sample1_NORMAL.bam /path/to/the/BAM/folder/Sample1_NORMAL.bam.bai ``` ### Genome @@ -104,8 +109,8 @@ Example ```bash Tumor Normal -c130863309_TUMOR c130863309_PBMC -c130889189_TUMOR c130889189_PBMC +Sample1_TUMOR Sample1_Normal +Sample2_TUMOR Sample1_Normal ``` #### 2. Tumor only mode @@ -146,23 +151,68 @@ Example: `--svcallers gridss` Example of Tumor_Normal calling mode ```bash -# preview the logan jobs that will run -nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -preview --vc --sv --cnv -# run a stub/dryrun of the logan jobs -nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" -stub --vc --sv --cnv -# launch a logan run on slurm with the test dataset -nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --sample_sheet samplesheet.tsv --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv +# Step 0: Set up + +sinteractive --mem=8g -N 1 -n 4 +module load ccbrpipeliner # v8 + +# set up directories + +DATADIR="/path/to/fastq/folder" + +# Step1: Initilalization + +logan init \ +--output logan_output + +# Step2: stub-run + +logan run \ +--output logan_output \ +--mode local -profile ci_stub \ +--genome hg38 \ +--sample_sheet samplesheet.txt \ +--fastq_file_input logan_fastq_input.txt \ +-stub --vc --sv --cnv + +# Step3: Full run +logan run \ +--output logan_output \ +--mode slurm -profile slurm \ +--genome hg38 \ +--sample_sheet samplesheet.txt \ +--fastq_file_input logan_fastq_input.txt \ +--vc --sv --cnv + +# NOTE: In case of globbing instead of using a fastq input sheet + +logan run \ +--output logan_output \ +--mode local -profile ci_stub \ +--genome hg38 \ +--sample_sheet samplesheet.txt \ +--fastq_input "/path/to/fastq/folder/*R{1,2}.fastq.gz" \ +-stub --vc --sv --cnv + +logan run \ +--output logan_output \ +--mode slurm -profile slurm \ +--genome hg38 \ +--sample_sheet samplesheet.txt \ +--fastq_input "/path/to/fastq/folder/*R{1,2}.fastq.gz" \ +--vc --sv --cnv + ``` Example of Tumor only calling mode ```bash # preview the logan jobs that will run -nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv +logan run --mode local -profile ci_stub --genome hg38 --outdir logan_output --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -preview --vc --sv --cnv # run a stub/dryrun of the logan jobs -nextflow run LOGAN/main.nf --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv +logan run --mode local -profile ci_stub --genome hg38 --outdir logan_output --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 -stub --vc --sv --cnv # launch a logan run on slurm with the test dataset -nextflow run LOGAN/main.nf --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv +logan run --mode slurm -profile slurm --genome hg38 --outdir logan_output --fastq_input "*R{1,2}.fastq.gz" --callers octopus,mutect2 --vc --sv --cnv ``` ### Pipeline Tools and Overview diff --git a/docs/index.md b/docs/index.md index 9900632..0e0b6b4 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,2 +1,2 @@ -# **_LOGAN-whoLe genOme-sequencinG Analysis pipeliNe_**. Call germline and somatic variants, CNVs, and SVs and annotate variants! +--8<-- "README.md" From 3a8ee5cfcf69e45c480e47cd0b6a3beabd6c29c9 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:16:53 -0400 Subject: [PATCH 4/7] chore: updated CHANGELOG.md; version --- CHANGELOG.md | 5 ++++- CITATION.cff | 4 ++-- VERSION | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5402276..521f020 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,7 @@ -## LOGAN development version +## LOGAN 0.3.2 +- Removed old bindpaths and fixed ` /gs10 doesn't exist` error (#106, @samarth8392) +- Increased pipeline walltime for slurm submission to 100 hours (#106, @samarth8392) +- Minor documentation updates for setup and running LOGAN (#106, @samarth8392) - Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: https://github.com/nextflow-io/nextflow/issues/5456) (#99, @samarth8392) - ## LOGAN 0.3.1 diff --git a/CITATION.cff b/CITATION.cff index d75fccf..c9f1b8a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -34,5 +34,5 @@ identifiers: - description: Archived snapshots of all versions type: doi value: 10.5281/zenodo.14907169 -version: v0.3.1 -date-released: "2025-05-28" +version: v0.3.2 +date-released: "2025-09-10" diff --git a/VERSION b/VERSION index 746bd19..d15723f 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.3.1-dev +0.3.2 From 6cf1256d10c8cdd91e2deea4aa315ebe4cefa7cb Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:19:03 -0400 Subject: [PATCH 5/7] fix: corrected issue no. in CHANGELOG.md --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 521f020..bc6751b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,7 @@ ## LOGAN 0.3.2 -- Removed old bindpaths and fixed ` /gs10 doesn't exist` error (#106, @samarth8392) -- Increased pipeline walltime for slurm submission to 100 hours (#106, @samarth8392) -- Minor documentation updates for setup and running LOGAN (#106, @samarth8392) +- Removed old bindpaths and fixed ` /gs10 doesn't exist` error (#107, @samarth8392) +- Increased pipeline walltime for slurm submission to 100 hours (#107, @samarth8392) +- Minor documentation updates for setup and running LOGAN (#107, @samarth8392) - Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: https://github.com/nextflow-io/nextflow/issues/5456) (#99, @samarth8392) - ## LOGAN 0.3.1 From 5efd949dcb5d28df7c6446eb3a64393124b6f290 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Wed, 10 Sep 2025 11:21:59 -0400 Subject: [PATCH 6/7] chore: undo version change --- CITATION.cff | 4 ++-- VERSION | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index c9f1b8a..d75fccf 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -34,5 +34,5 @@ identifiers: - description: Archived snapshots of all versions type: doi value: 10.5281/zenodo.14907169 -version: v0.3.2 -date-released: "2025-09-10" +version: v0.3.1 +date-released: "2025-05-28" diff --git a/VERSION b/VERSION index d15723f..746bd19 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.3.2 +0.3.1-dev From 2c3fc6dcb091537c3e8170a71f917ac8c8a5a63d Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 10 Sep 2025 12:04:56 -0400 Subject: [PATCH 7/7] docs: fix CHANGELOG.md -- new items go under development header --- CHANGELOG.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc6751b..aa82f94 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,9 +1,13 @@ -## LOGAN 0.3.2 +## LOGAN development version + - Removed old bindpaths and fixed ` /gs10 doesn't exist` error (#107, @samarth8392) - Increased pipeline walltime for slurm submission to 100 hours (#107, @samarth8392) - Minor documentation updates for setup and running LOGAN (#107, @samarth8392) + +## LOGAN 0.3.2 + - Uses Nextflow v25 for logan run; fixes the bug in stub run in nf v24.10 (see: https://github.com/nextflow-io/nextflow/issues/5456) (#99, @samarth8392) -- + ## LOGAN 0.3.1 - Improve help message for `logan run`. (#97, @kelly-sovacool)