From b8cb37019096f7f7e20c424fbf2d1886ca3b19de Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Fri, 17 Jan 2025 11:27:33 +0100 Subject: [PATCH] Addressed final reviewer suggestion for version 1.0.0 --- .nf-core.yml | 1 + CHANGELOG.md | 2 +- README.md | 2 +- docs/images/rangeland_diagram.svg | 4 ++++ docs/output.md | 13 ++++++++----- nextflow.config | 2 +- workflows/rangeland.nf | 2 +- 7 files changed, 17 insertions(+), 9 deletions(-) create mode 100644 docs/images/rangeland_diagram.svg diff --git a/.nf-core.yml b/.nf-core.yml index 586b308..aca765b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -15,4 +15,5 @@ template: outdir: . skip_features: - igenomes + - fastqc version: 1.0.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 259eb81..313cdac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - [date] +## v1.0.0 - [2025-01-17] First release of `nf-core/rangeland`. This work is a continuation, and nf-core port, of the [original version of this pipeline](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland). diff --git a/README.md b/README.md index 8c2e151..3e1db21 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ The pipeline processes satellite imagery alongside auxiliary data in multiple st ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. To run, satellite imagery, water vapor data, a digital elevation model, endmember definitions, a datacube specification, and a area-of-interest specification are required as input data. Please refer to the [usage documentation](https://nf-co.re/rangeland/usage) for details on the input structure. diff --git a/docs/images/rangeland_diagram.svg b/docs/images/rangeland_diagram.svg new file mode 100644 index 0000000..b681a5f --- /dev/null +++ b/docs/images/rangeland_diagram.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/docs/output.md b/docs/output.md index 8769c5a..1c4bfed 100644 --- a/docs/output.md +++ b/docs/output.md @@ -7,7 +7,7 @@ This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. -Note that running this pipeline with `--publish_dir_enabled false` will prevent any module from publishing its output. See [Usage](usage.md#module-output-publishing) for details +Note that running this pipeline with `--publish_dir_enabled false` will prevent any module from publishing its output. See [Usage](./usage.md#module-output-publishing) for details. ## Pipeline overview @@ -27,13 +27,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d

Output files

- `untar/` - - ``: directory containing symlinks to decompressed digital elevation input data. + - `/`: directory containing symlinks to decompressed digital elevation input data. Only present if a tar archive was provided for the digital elevation model. Name of the directory derived from archive contents. - - ``: directory containing symlinks to decompressed water vapor input data. + - `/`: directory containing symlinks to decompressed water vapor input data. Only present if a tar archive was provided for water vapor data. Name of the directory derived from archive contents. - - ``: directory containing symlinks to decompressed satellite imagery input data. + - `/`: directory containing symlinks to decompressed satellite imagery input data. Only present if a tar archive was provided for satellite data. Name of the directory derived from archive contents. @@ -90,7 +90,10 @@ Logs and analysis-ready-data (ARD) are generated using the [force-l2ps](https:// Logs can be consulted for debugging purposes. ARD may be collected as a basis for other remote sensing workflows. The ARD in `level2_ard/` consist two `.tif` files per initial input image, a quality data file and the atmospherically corrected satellite data. -Note that the `.tif` files are only published when the `--save_ard` parameter is set to `true` to avoid bloating the storage. + +:::note +The `.tif` files are only published when the `--save_ard` parameter is set to `true` to avoid bloating the storage. +::: ### Higher-level-Processing diff --git a/nextflow.config b/nextflow.config index 8370752..3f7ff40 100644 --- a/nextflow.config +++ b/nextflow.config @@ -269,7 +269,7 @@ manifest { email: 'felix.kummer@hu-berlin.de', github: 'https://github.com/Felix-Kummer', contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') - orcid: '' + orcid: 'https://orcid.org/0009-0007-1154-6980' ], ] homePage = 'https://github.com/nf-core/rangeland' diff --git a/workflows/rangeland.nf b/workflows/rangeland.nf index 93b1b40..8cc12a1 100644 --- a/workflows/rangeland.nf +++ b/workflows/rangeland.nf @@ -93,7 +93,7 @@ workflow RANGELAND { } data.ifEmpty { - error "No directories found!" + error "[nf-core/rangeland] ERROR: No directories found in input path or .tar file!" } // Determine type of params.dem and extract when neccessary