From 8d4839f52ef40ab954e1166a0f37a71af5e2f3f9 Mon Sep 17 00:00:00 2001 From: Jonas Ibn-Salem Date: Fri, 21 Jul 2023 09:50:06 +0200 Subject: [PATCH 01/19] readd GNU license file --- LICENSE | 674 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 674 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. From 6159cc4a0a701ff63fcfc363abffac2eb8684d2d Mon Sep 17 00:00:00 2001 From: "Ibn-Salem, Jonas" Date: Sat, 22 Jul 2023 11:18:16 +0200 Subject: [PATCH 02/19] Update file 01_qc.nf --- modules/01_qc.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/01_qc.nf b/modules/01_qc.nf index 0737723..c50c11f 100644 --- a/modules/01_qc.nf +++ b/modules/01_qc.nf @@ -40,7 +40,7 @@ process FASTQC_PARSER { path("qc_table.txt"), emit: qc_table """ - easy-fuse qc-parser -i $fastq1_qc_data $fastq1_qc_data -o qc_table.txt + easy-fuse qc-parser -i $fastq1_qc_data $fastq2_qc_data -o qc_table.txt """ } From 9f97cd2b0d8d9d1a54bd764797368f5119b48f71 Mon Sep 17 00:00:00 2001 From: priesgo Date: Mon, 31 Jul 2023 13:59:27 +0200 Subject: [PATCH 03/19] bump version to 2.0.1 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index a280bec..2a5d82a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,7 +17,7 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -VERSION = '2.0.0a1' +VERSION = '2.0.1' manifest { name = 'TRON-Bioinformatics/easy-fuse-workflow' From ca47ce654bfc0b2d446c1992dc9b9726dab06911 Mon Sep 17 00:00:00 2001 From: priesgo Date: Mon, 31 Jul 2023 14:09:40 +0200 Subject: [PATCH 04/19] integrate easyfuse-src via bioconda --- environments/easyfuse_src.yml | 7 +++++++ environments/requantification.yml | 1 + environments/summarize_data.yml | 12 ------------ modules/01_qc.nf | 2 +- modules/02_alignment.nf | 2 +- modules/04_joint_fusion_calling.nf | 4 ++-- modules/05_requantification.nf | 10 +++++++--- modules/06_summarize.nf | 2 +- 8 files changed, 20 insertions(+), 20 deletions(-) create mode 100644 environments/easyfuse_src.yml delete mode 100644 environments/summarize_data.yml diff --git a/environments/easyfuse_src.yml b/environments/easyfuse_src.yml new file mode 100644 index 0000000..02c0ef2 --- /dev/null +++ b/environments/easyfuse_src.yml @@ -0,0 +1,7 @@ +name: easyfuse_src +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::pyeasyfuse=2.0.3 diff --git a/environments/requantification.yml b/environments/requantification.yml index 9bb3ca9..05e83e2 100644 --- a/environments/requantification.yml +++ b/environments/requantification.yml @@ -6,3 +6,4 @@ channels: dependencies: - bioconda::star=2.6.1d - bioconda::samtools=1.9.0 + - bioconda::pyeasyfuse=2.0.3 diff --git a/environments/summarize_data.yml b/environments/summarize_data.yml deleted file mode 100644 index 0973bdc..0000000 --- a/environments/summarize_data.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: summarize_data -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - conda-forge::r-base=4.2.1 - - conda-forge::r-optparse=1.7.3 - - conda-forge::r-randomforest=4.7_1.1 - - conda-forge::r-tidyverse=1.3.2 - - conda-forge::r-xml=3.99_0.14 - diff --git a/modules/01_qc.nf b/modules/01_qc.nf index c50c11f..90678aa 100644 --- a/modules/01_qc.nf +++ b/modules/01_qc.nf @@ -28,7 +28,7 @@ process FASTQC_PARSER { memory "8g" tag "${name}" -// conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), diff --git a/modules/02_alignment.nf b/modules/02_alignment.nf index c0562f5..d3ea1c4 100644 --- a/modules/02_alignment.nf +++ b/modules/02_alignment.nf @@ -45,7 +45,7 @@ process READ_FILTER { memory "8g" tag "${name}" - //conda (params.enable_conda ? "bioconda::easyfuse=0.1.0" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam) diff --git a/modules/04_joint_fusion_calling.nf b/modules/04_joint_fusion_calling.nf index 647698d..d399b8f 100644 --- a/modules/04_joint_fusion_calling.nf +++ b/modules/04_joint_fusion_calling.nf @@ -4,7 +4,7 @@ process FUSION_PARSER { memory "8g" tag "${name}" - //conda (params.enable_conda ? "bioconda::easyfuse=0.1.0" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusion_catcher_1), path(fusion_catcher_2), path(star_fusion) @@ -30,7 +30,7 @@ process FUSION_ANNOTATION { memory "8g" tag "${name}" - //conda (params.enable_conda ? "bioconda::easyfuse=0.1.0" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusions) diff --git a/modules/05_requantification.nf b/modules/05_requantification.nf index f85b8cc..c3500ba 100755 --- a/modules/05_requantification.nf +++ b/modules/05_requantification.nf @@ -4,7 +4,10 @@ process STAR_INDEX { memory "8g" tag "${name}" - //conda (params.enable_conda ? "bioconda::easyfuse=0.1.0" : null) + // TODO: do we really need STAR and samtools here too? + // if yes, OK but we need to add these two dependencies to the easyfuse bioconda package + // if no, then here we need to use the easyfuse_src.yml environment and we have to remove + // pyeasyfuse from requantification.yml conda (params.enable_conda ? "${baseDir}/environments/requantification.yml" : null) input: @@ -30,7 +33,7 @@ process FUSION_FILTER { memory "8g" tag "${name}" - //conda (params.enable_conda ? "bioconda::easyfuse=0.1.0" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam), path(annot_fusions_1), path(annot_fusions_2), path(read_stats) @@ -87,7 +90,8 @@ process READ_COUNT { cpus 6 memory "50g" tag "${name}" - //publishDir "${params.output}/${name}", mode: 'copy' + + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam), path(bam_index), path(read_stats) diff --git a/modules/06_summarize.nf b/modules/06_summarize.nf index 8fe398e..3ebb8dc 100755 --- a/modules/06_summarize.nf +++ b/modules/06_summarize.nf @@ -5,7 +5,7 @@ process SUMMARIZE_DATA { tag "${name}" publishDir "${params.output}/${name}", mode: 'copy' - conda (params.enable_conda ? "${baseDir}/environments/summarize_data.yml" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusions), path(annot_csv), path(annot_fasta), path(cpms), path(counts), path(read_stats) From bab0258f3f770ebef3ff6f7e2cca7b0942f47e28 Mon Sep 17 00:00:00 2001 From: priesgo Date: Mon, 31 Jul 2023 14:37:47 +0200 Subject: [PATCH 05/19] update installation documentation --- README.md | 36 +++++++++++++++++++----------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index fe4f262..4b5ea2e 100644 --- a/README.md +++ b/README.md @@ -37,29 +37,21 @@ tar xvfz easyfuse_ref_v2.tar.gz ``` -### Download nextflow pipeline and install EasyFuse package +### Install the nextflow pipeline -Next, you have to download the nextflow pipeline including the EasyFuse package source dir. +There are two alternatives, manually install the workflow or let Nexftlow handle this via the GitHub repository. +To install manually: ``` git clone --recurse-submodules https://github.com/TRON-Bioinformatics/EasyFuse.git - cd EasyFuse +``` -cd easyfuse_src - -# Create virtual environment using Python3.7 (only works on Python3.7) -python3.7 -m venv env/ - -# Activate environment -source env/bin/activate - -# Install poetry for easy installation -pip install poetry - -# Install EasyFuse package using poetry -poetry install +To install with Netxflow (only available from release 2.0.1): ``` +nextflow run tron-bioinformatics/easyfuse -t x.y.z --help +``` +where x.y.z corresponds to an EasyFuse release. ### Run the pipeline @@ -74,7 +66,7 @@ sample_01 /path/to/sample_01_R1.fastq.gz /path/to/sample_01_R2.fastq.gz ``` -Start the pipeline as follows +Start the pipeline as follows if you installed manually ``` nextflow main.nf \ @@ -84,6 +76,16 @@ nextflow main.nf \ --output /path/to/output_folder ``` + +Or as follows if you installed it via Nextflow (only available from release 2.0.1): +``` +nextflow run tron-bioinformatics/easyfuse -t x.y.z \ + -profile conda \ + --reference /path/to/reference/folder \ + --input_files /path/to/input_table_file \ + --output /path/to/output_folder +``` + ### Output format EasyFuse creates an output folder for each input sample containing the following files: From 3ef7a67d73284ea40f7150bdc9b51887049a8b86 Mon Sep 17 00:00:00 2001 From: priesgo Date: Mon, 31 Jul 2023 14:51:21 +0200 Subject: [PATCH 06/19] document how to increase the software version --- CONTRIBUTE.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CONTRIBUTE.md b/CONTRIBUTE.md index 30e951a..85294af 100644 --- a/CONTRIBUTE.md +++ b/CONTRIBUTE.md @@ -6,3 +6,7 @@ After the EasyFuse Python package is installed as described in the README, run the integration tests with `make`. You may need to edit the test scripts to use an appropriate reference folder in `--reference`. + +## Prepare a new release + +Increase the version in the property `VERSION` in the file `nextflow.config`. From 7afed72732a648dad67a0b90126e3fe0b76d30c1 Mon Sep 17 00:00:00 2001 From: priesgo Date: Tue, 1 Aug 2023 14:24:45 +0200 Subject: [PATCH 07/19] confirm the requantification dependencies --- modules/05_requantification.nf | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/modules/05_requantification.nf b/modules/05_requantification.nf index c3500ba..25ba8e8 100755 --- a/modules/05_requantification.nf +++ b/modules/05_requantification.nf @@ -4,10 +4,7 @@ process STAR_INDEX { memory "8g" tag "${name}" - // TODO: do we really need STAR and samtools here too? - // if yes, OK but we need to add these two dependencies to the easyfuse bioconda package - // if no, then here we need to use the easyfuse_src.yml environment and we have to remove - // pyeasyfuse from requantification.yml + // NOTE: we really need STAR and samtools here, these are not added as dependencies to the bioconda package conda (params.enable_conda ? "${baseDir}/environments/requantification.yml" : null) input: From 59a71c18e518be2117a67a50c8a5a9957cf053be Mon Sep 17 00:00:00 2001 From: priesgo Date: Tue, 1 Aug 2023 14:25:35 +0200 Subject: [PATCH 08/19] remove not needed submodule --- .gitmodules | 4 ---- easyfuse_src | 1 - 2 files changed, 5 deletions(-) delete mode 100644 .gitmodules delete mode 160000 easyfuse_src diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index f5f8d36..0000000 --- a/.gitmodules +++ /dev/null @@ -1,4 +0,0 @@ -[submodule "easyfuse_src"] - path = easyfuse_src - url = https://github.com/TRON-Bioinformatics/easyfuse-src.git - branch = master \ No newline at end of file diff --git a/easyfuse_src b/easyfuse_src deleted file mode 160000 index 6e37df6..0000000 --- a/easyfuse_src +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 6e37df6b6ffab3a5027d36583851ea58020ef862 From fefb52ad4938570d9967986d4fe0b7e48668fd79 Mon Sep 17 00:00:00 2001 From: priesgo Date: Tue, 1 Aug 2023 14:26:24 +0200 Subject: [PATCH 09/19] update readme --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 4b5ea2e..be534bd 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,6 @@ For maximal sensitivity, we recommend using an older EasyFuse release with five - Publication: [Weber D, Ibn-Salem J, Sorn P, et al. Nat Biotechnol. 2022](https://doi.org/10.1038/s41587-022-01247-9) - - ## Usage ### Dependencies From e30c57b9e3b0f702047df3ea59df69ff4655bc18 Mon Sep 17 00:00:00 2001 From: priesgo Date: Tue, 1 Aug 2023 14:38:34 +0200 Subject: [PATCH 10/19] add a development mode that still employs conda but not for the easyfuse package --- environments/requantification_wo_easyfuse.yml | 8 ++++++++ modules/01_qc.nf | 2 +- modules/02_alignment.nf | 2 +- modules/04_joint_fusion_calling.nf | 4 ++-- modules/05_requantification.nf | 13 +++++++++---- modules/06_summarize.nf | 2 +- nextflow.config | 3 +++ 7 files changed, 25 insertions(+), 9 deletions(-) create mode 100644 environments/requantification_wo_easyfuse.yml diff --git a/environments/requantification_wo_easyfuse.yml b/environments/requantification_wo_easyfuse.yml new file mode 100644 index 0000000..9bb3ca9 --- /dev/null +++ b/environments/requantification_wo_easyfuse.yml @@ -0,0 +1,8 @@ +name: requantification +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.6.1d + - bioconda::samtools=1.9.0 diff --git a/modules/01_qc.nf b/modules/01_qc.nf index 90678aa..6db9c9d 100644 --- a/modules/01_qc.nf +++ b/modules/01_qc.nf @@ -28,7 +28,7 @@ process FASTQC_PARSER { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), diff --git a/modules/02_alignment.nf b/modules/02_alignment.nf index d3ea1c4..4eca088 100644 --- a/modules/02_alignment.nf +++ b/modules/02_alignment.nf @@ -45,7 +45,7 @@ process READ_FILTER { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam) diff --git a/modules/04_joint_fusion_calling.nf b/modules/04_joint_fusion_calling.nf index d399b8f..52cae4c 100644 --- a/modules/04_joint_fusion_calling.nf +++ b/modules/04_joint_fusion_calling.nf @@ -4,7 +4,7 @@ process FUSION_PARSER { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusion_catcher_1), path(fusion_catcher_2), path(star_fusion) @@ -30,7 +30,7 @@ process FUSION_ANNOTATION { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusions) diff --git a/modules/05_requantification.nf b/modules/05_requantification.nf index 25ba8e8..dc8c535 100755 --- a/modules/05_requantification.nf +++ b/modules/05_requantification.nf @@ -5,7 +5,12 @@ process STAR_INDEX { tag "${name}" // NOTE: we really need STAR and samtools here, these are not added as dependencies to the bioconda package - conda (params.enable_conda ? "${baseDir}/environments/requantification.yml" : null) + if (params.disable_pyeasyfuse_conda) { + conda (params.enable_conda ? "${baseDir}/environments/requantification_wo_easyfuse.yml" : null) + } + else { + conda (params.enable_conda ? "${baseDir}/environments/requantification.yml" : null) + } input: tuple val(name), path(annot_csv), path(annot_fasta) @@ -30,7 +35,7 @@ process FUSION_FILTER { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam), path(annot_fusions_1), path(annot_fusions_2), path(read_stats) @@ -54,7 +59,7 @@ process STAR_CUSTOM { memory "32g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/requantification.yml" : null) + conda (params.enable_conda ? "${baseDir}/environments/requantification_wo_easyfuse.yml" : null) input: tuple val(name), path(fastq1), file(fastq2), path(star_index) @@ -88,7 +93,7 @@ process READ_COUNT { memory "50g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(bam), path(bam_index), path(read_stats) diff --git a/modules/06_summarize.nf b/modules/06_summarize.nf index 3ebb8dc..62aad2a 100755 --- a/modules/06_summarize.nf +++ b/modules/06_summarize.nf @@ -5,7 +5,7 @@ process SUMMARIZE_DATA { tag "${name}" publishDir "${params.output}/${name}", mode: 'copy' - conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) + conda (params.enable_conda && ! params.disable_pyeasyfuse_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), path(fusions), path(annot_csv), path(annot_fasta), path(cpms), path(counts), path(read_stats) diff --git a/nextflow.config b/nextflow.config index 2a5d82a..6fa9e17 100644 --- a/nextflow.config +++ b/nextflow.config @@ -43,6 +43,9 @@ params.annotation_db = "${params.reference}/Homo_sapiens.GRCh38.86.gff3.db" params.reference_tsl = "${params.reference}/Homo_sapiens.GRCh38.86.gtf.tsl" params.model_pred = "${baseDir}/data/model/Fusion_modeling_FFPE_train_v35.random_forest.model_full_data.EF_requant_type.rds" +// use this to avoid +params.disable_pyeasyfuse_conda = false + params.help_message = """ From 00ca67995bc79737becd1831e13597003c63bbb8 Mon Sep 17 00:00:00 2001 From: priesgo Date: Tue, 1 Aug 2023 14:42:23 +0200 Subject: [PATCH 11/19] update developer guide --- CONTRIBUTE.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CONTRIBUTE.md b/CONTRIBUTE.md index 85294af..28d78b7 100644 --- a/CONTRIBUTE.md +++ b/CONTRIBUTE.md @@ -10,3 +10,12 @@ You may need to edit the test scripts to use an appropriate reference folder in ## Prepare a new release Increase the version in the property `VERSION` in the file `nextflow.config`. + +## Test the integration of easyfuse-src + +The Python and R code are distributed as a Python package and this is imported in +EasyFuse pipeline via conda. But, for development purposes the import of this +package can be skipped while all other dependencies are still managed via conda. + +Use the flag `--disable_pyeasyfuse_conda`, this will rely on whatever version of +pyeasyfuse has been installed on your environment. From 88b4f5006b02d29078809f66bc413bde1f5f0c5e Mon Sep 17 00:00:00 2001 From: Patrick Sorn Date: Mon, 7 Aug 2023 10:54:03 +0200 Subject: [PATCH 12/19] Fixed environment dependencies --- environments/easyfuse_src.yml | 1 + environments/qc.yml | 1 - environments/requantification.yml | 1 - environments/requantification_wo_easyfuse.yml | 2 +- modules/01_qc.nf | 2 +- 5 files changed, 3 insertions(+), 4 deletions(-) diff --git a/environments/easyfuse_src.yml b/environments/easyfuse_src.yml index 02c0ef2..73593be 100644 --- a/environments/easyfuse_src.yml +++ b/environments/easyfuse_src.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::pyeasyfuse=2.0.3 + - bioconda::skewer=0.2.2 diff --git a/environments/qc.yml b/environments/qc.yml index e0bd27f..99c0941 100644 --- a/environments/qc.yml +++ b/environments/qc.yml @@ -5,4 +5,3 @@ channels: - defaults dependencies: - bioconda::fastqc=0.11.9 - - bioconda::skewer=0.2.2 diff --git a/environments/requantification.yml b/environments/requantification.yml index 05e83e2..ac0fb16 100644 --- a/environments/requantification.yml +++ b/environments/requantification.yml @@ -5,5 +5,4 @@ channels: - defaults dependencies: - bioconda::star=2.6.1d - - bioconda::samtools=1.9.0 - bioconda::pyeasyfuse=2.0.3 diff --git a/environments/requantification_wo_easyfuse.yml b/environments/requantification_wo_easyfuse.yml index 9bb3ca9..bc04edb 100644 --- a/environments/requantification_wo_easyfuse.yml +++ b/environments/requantification_wo_easyfuse.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: - bioconda::star=2.6.1d - - bioconda::samtools=1.9.0 + - bioconda::samtools=1.9.0 \ No newline at end of file diff --git a/modules/01_qc.nf b/modules/01_qc.nf index 6db9c9d..4333149 100644 --- a/modules/01_qc.nf +++ b/modules/01_qc.nf @@ -49,7 +49,7 @@ process SKEWER { memory "8g" tag "${name}" - conda (params.enable_conda ? "${baseDir}/environments/qc.yml" : null) + conda (params.enable_conda ? "${baseDir}/environments/easyfuse_src.yml" : null) input: tuple val(name), From 1e582a096bd57233368fca0b2aed16237dcbb2e1 Mon Sep 17 00:00:00 2001 From: Patrick Sorn Date: Mon, 7 Aug 2023 11:38:35 +0200 Subject: [PATCH 13/19] Updated README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index be534bd..29162e6 100644 --- a/README.md +++ b/README.md @@ -41,11 +41,11 @@ There are two alternatives, manually install the workflow or let Nexftlow handle To install manually: ``` -git clone --recurse-submodules https://github.com/TRON-Bioinformatics/EasyFuse.git +git clone https://github.com/TRON-Bioinformatics/EasyFuse.git cd EasyFuse ``` -To install with Netxflow (only available from release 2.0.1): +To install with Nextflow (only available from release 2.0.1): ``` nextflow run tron-bioinformatics/easyfuse -t x.y.z --help ``` From a1034714445ed2561cf0f270b4b1c07403bc7d1c Mon Sep 17 00:00:00 2001 From: "Sorn, Patrick" Date: Wed, 9 Aug 2023 09:47:32 +0200 Subject: [PATCH 14/19] Update .gitlab-ci.yml file --- .gitlab-ci.yml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 .gitlab-ci.yml diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000..7d53156 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,9 @@ +easyfuse-pipeline: + image: continuumio/miniconda:4.7.10 + stage: build + tags: + - docker + script: + - conda install -c bioconda nextflow + - bash test/scripts/test_00.sh + From d1cf5ca6c85bc57ccba89f4ecfa98af12e9972d1 Mon Sep 17 00:00:00 2001 From: "Sorn, Patrick" Date: Wed, 9 Aug 2023 13:13:39 +0200 Subject: [PATCH 15/19] Removed job runner for docker --- .gitlab-ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 7d53156..686d664 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,8 +1,6 @@ easyfuse-pipeline: image: continuumio/miniconda:4.7.10 stage: build - tags: - - docker script: - conda install -c bioconda nextflow - bash test/scripts/test_00.sh From 7acd58da2ae8be86c37a1f0566b1c7d73a72cf0b Mon Sep 17 00:00:00 2001 From: Jonas Ibn-Salem Date: Wed, 9 Aug 2023 13:46:45 +0200 Subject: [PATCH 16/19] fix nextflow parameter -r in README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 29162e6..3a15482 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ cd EasyFuse To install with Nextflow (only available from release 2.0.1): ``` -nextflow run tron-bioinformatics/easyfuse -t x.y.z --help +nextflow run tron-bioinformatics/easyfuse -r x.y.z --help ``` where x.y.z corresponds to an EasyFuse release. @@ -77,7 +77,7 @@ nextflow main.nf \ Or as follows if you installed it via Nextflow (only available from release 2.0.1): ``` -nextflow run tron-bioinformatics/easyfuse -t x.y.z \ +nextflow run tron-bioinformatics/easyfuse -r x.y.z \ -profile conda \ --reference /path/to/reference/folder \ --input_files /path/to/input_table_file \ From f8ffd71564f5b410616a9e54ed5348922b2175b3 Mon Sep 17 00:00:00 2001 From: Jonas Ibn-Salem Date: Wed, 9 Aug 2023 13:48:44 +0200 Subject: [PATCH 17/19] add -with-conda option in RADME --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3a15482..cacd792 100644 --- a/README.md +++ b/README.md @@ -68,7 +68,7 @@ Start the pipeline as follows if you installed manually ``` nextflow main.nf \ - -profile conda \ + -profile conda -with-conda \ --reference /path/to/reference/folder \ --input_files /path/to/input_table_file \ --output /path/to/output_folder @@ -78,7 +78,7 @@ nextflow main.nf \ Or as follows if you installed it via Nextflow (only available from release 2.0.1): ``` nextflow run tron-bioinformatics/easyfuse -r x.y.z \ - -profile conda \ + -profile conda -with-conda \ --reference /path/to/reference/folder \ --input_files /path/to/input_table_file \ --output /path/to/output_folder From 7bd60b121a947e243459007e2c1c99dcf911afa3 Mon Sep 17 00:00:00 2001 From: "Sorn, Patrick" Date: Wed, 9 Aug 2023 14:05:39 +0200 Subject: [PATCH 18/19] Update .gitlab-ci.yml file --- .gitlab-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 686d664..c25420b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,6 +2,6 @@ easyfuse-pipeline: image: continuumio/miniconda:4.7.10 stage: build script: - - conda install -c bioconda nextflow + - conda install -c bioconda nextflow=20.10.0 - bash test/scripts/test_00.sh From 27ccd1139b061f2a7699f5b43a7e84efade63023 Mon Sep 17 00:00:00 2001 From: "Sorn, Patrick" Date: Wed, 9 Aug 2023 14:33:52 +0200 Subject: [PATCH 19/19] Updated miniconda version --- .gitlab-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c25420b..7f7e7d9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,5 +1,5 @@ easyfuse-pipeline: - image: continuumio/miniconda:4.7.10 + image: continuumio/miniconda3:23.5.2-0 stage: build script: - conda install -c bioconda nextflow=20.10.0