diff --git a/docs/Tutorials/Getting-Start.md b/docs/Tutorials/Getting-Start.md index 71f59b6..96ed242 100644 --- a/docs/Tutorials/Getting-Start.md +++ b/docs/Tutorials/Getting-Start.md @@ -79,19 +79,20 @@ Once Nextflow starts running: ``` bash N E X T F L O W ~ version 24.04.2 -Launching `EBISPOT/gwas-sumstats-harmoniser` [goofy_tuckerman] DSL2 - revision: 118e098430 +Launching `https://github.com/EBISPOT/gwas-sumstats-harmoniser` [maniac_mestorf] DSL2 - revision: 67198bb9e7 Harmonizing the file ~/.nextflow/assets/EBISPOT/gwas-sumstats-harmoniser/test_data/random_name.tsv -executor > local (9) -[ec/f4716a] NFC…ATALOGHARM:major_direction:map_to_build (random_name) | 1 of 1 ✔ -[7b/52d159] NFC…HARM:major_direction:ten_percent_counts (random_name) | 2 of 2 ✔ -[9a/a0478c] NFC…:major_direction:ten_percent_counts_sum (random_name) | 1 of 1 ✔ -[- ] NFC…WASCATALOGHARM:major_direction:generate_strand_counts - -[- ] NFC…ASCATALOGHARM:major_direction:summarise_strand_counts - -[71/6c263a] NFC…GWASCATALOGHARM:main_harm:harmonization (random_name) | 2 of 2 ✔ -[77/e0224e] NFC…OGHARM:main_harm:concatenate_chr_splits (random_name) | 1 of 1 ✔ -[6f/9db381] NFC…HARM:GWASCATALOGHARM:quality_control:qc (random_name) | 1 of 1 ✔ -[c7/5c00d2] NFC…GHARM:quality_control:harmonization_log (random_name) | 1 of 1 ✔ +executor > local (13) +[9a/05e067] NFC…ATALOGHARM:major_direction:map_to_build (random_name) | 1 of 1 ✔ +[cc/fef59c] NFC…ajor_direction:ten_percent_counts (random_name_chr22) | 2 of 2 ✔ +[46/626f6f] NFC…:major_direction:ten_percent_counts_sum (random_name) | 1 of 1 ✔ +[1c/b92ff2] NFC…_direction:generate_strand_counts (random_name_chr22) | 2 of 2 ✔ +[b7/3f81cb] NFC…major_direction:summarise_strand_counts (random_name) | 1 of 1 ✔ +[67/216e41] NFC…TALOGHARM:main_harm:harmonization (random_name_chr22) | 2 of 2 ✔ +[a9/336d51] NFC…OGHARM:main_harm:concatenate_chr_splits (random_name) | 1 of 1 ✔ +[64/8a8fec] NFC…HARM:GWASCATALOGHARM:quality_control:qc (random_name) | 1 of 1 ✔ +[6e/fb619c] NFC…GHARM:quality_control:harmonization_log (random_name) | 1 of 1 ✔ +[48/1ae6d4] NFC…OGHARM:quality_control:update_meta_yaml (random_name) | 1 of 1 ✔ [chr1, chr22, is being harmonized] ``` @@ -99,26 +100,28 @@ In your current directory, you will find a folder named `random_name` that conta ```text ./random_name/ -├── 1.merged -├── 22.merged -├── final -│   ├── harmonised.qc.tsv -│   ├── harmonised.tsv -│   ├── random_name.h.tsv.gz (Final output) -│   ├── random_name.h.tsv.gz-meta.yaml (Final output) -│   ├── random_name.h.tsv.gz.tbi (Final output) -│   ├── random_name.running.log (Final output) -│   └── report.txt -├── harmonization +├── 1_map_to_build +│   ├── 1.merged +│   ├── 22.merged +│   ├── random_name.tsv-meta.yaml +│   └── unmapped +├── 2_ten_sc +│   ├── ten_percent_chr1.sc +│   └── ten_percent_chr22.sc +├── 4_harmonization │   ├── chr1.merged.hm │   ├── chr1.merged.log.tsv.gz │   ├── chr22.merged.hm │   └── chr22.merged.log.tsv.gz -├── random_name.tsv-meta.yaml -├── ten_percent_total_strand_count.tsv -├── ten_sc -│   ├── ten_percent_chr1.sc -│   └── ten_percent_chr22.sc -└── unmapped +├── 5_qc +│   ├── harmonised.qc.tsv +│   ├── harmonised.tsv +│   └── report.txt +├── final +│   ├── random_name.h.tsv.gz +│   ├── random_name.h.tsv.gz-meta.yaml +│   ├── random_name.h.tsv.gz.tbi +│   └── random_name.running.log +└── ten_percent_total_strand_count.tsv ``` -This output confirms that the pipeline has successfully executed and is ready to process larger real datasets. +This output confirms that the pipeline has been successfully executed and is ready to process larger real datasets.