Merge branch 'CCBR:main' into main

Author: ccbr-bot[bot]

CHANGELOG.md

@@ -1,5 +1,12 @@
 ## ASPEN development version
 
+## ASPEN 1.4.0
+
+- Add structured pipeline state tracking: a `pipeline.status.json` sidecar and `pipeline.{running,completed,failed,canceled}` marker files are now written to `WORKDIR` during `run`, with a live progress monitor that periodically updates `pipeline.running` with a step-completion percentage; a best-effort `jobby` TSV summary (`snakemake.log.jobby`) is now also generated when Slurm submission fails before Snakemake starts. Consolidated shared logging/banner/version-tag helper functions into a new staged library (`workflow/scripts/ccbr_pipeline_logging.sh`, slated for future migration to `ccbr_tools`); redesigned the `--version`/banner output. (#119, @kopardev)
+- Fix a bug where a fully successful run could be reported as `failed`: the Snakemake `onsuccess`/`onerror` telemetry hook (`jobby`/`spooker`) could crash on a stale `jobby` inherited from the submitting shell's environment, which Snakemake treated as fatal even though every rule had already completed. `submit_script.sbatch` now starts from a clean module environment (`module purge`) and the telemetry hook explicitly loads the pinned `ccbr_tools` install (fixing both `PATH` and `PYTHONPATH`) and is now non-fatal. `pipeline.{running,completed,failed,canceled}` marker files are also now human-readable instead of empty. (#144, @kopardev)
+- Fix the `Genome:` line in the run summary to reflect the genome configured in the workdir's `config.yaml` instead of the `-g`/`--genome` CLI flag or its default, which only apply to `init`/`reconfig`. (@kopardev)
+- Remove a leftover ASCII-art banner in `init.smk` that duplicated the redesigned `--version`/banner output on every Snakemake invocation. (@kopardev)
+
 ## ASPEN 1.3.0
 
 - Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both `dedup.bam` (PCR/optical duplicates removed) and `filtered.bam` (duplicates retained, labeled `nondedup`), written to separate `dedup`/`nondedup` output subfolders under `visualization/` and `peaks/{peakcaller}/{fixed_width/counts,DiffATAC}/`; previously only the duplicate-retaining `filtered.bam` was used. `dedup` is recommended for standard differential accessibility testing. (#138, @kopardev)

CITATION.cff

@@ -29,5 +29,5 @@ identifiers:
     type: doi
     value: 10.5281/zenodo.13755867
 doi: 10.5281/zenodo.13755867
-version: v1.3.0
-date-released: "2026-09-17"
+version: v1.4.0
+date-released: "2026-09-21"

README.md

@@ -10,9 +10,11 @@
 ## QuickStart guide
 
 ```bash
-module load ccbrpipeliner/7
+module load ccbrpipeliner
 ```
 
+> **Note**: This is illustrative example output captured at doc-writing time — exact values (e.g. `pipeline_home`, `git commit/tag`, `aspen_version`) will differ depending on which ASPEN version/branch is installed at your site. Run `aspen --help` yourself to see the current values for your installation.
+
 ```bash
 aspen --help
 ```
@@ -21,11 +23,13 @@ aspen --help
 ##########################################################################################
 
 Welcome to
-____ ____ ___  ____ _  _
-|__| [__  |__] |___ |\ |
-|  | ___] |    |___ | \|    v1.2.0
 
-A_TAC_S_eq A_nalysis P_ip_E_li_N_e
+╔══════════════════════════════════╗
+║  ASPEN PIPELINE                  ║
+║  v1.3.0                          ║
+╚══════════════════════════════════╝
+
+ATAC-Seq Analysis Pipeline
 
 ##########################################################################################
 
@@ -41,14 +45,16 @@ Here is a list of genome supported by aspen:
   * mm10          [Mouse]
   * mmul10        [Macaca mulatta(Rhesus monkey) or rheMac10]
   * bosTau9       [Bos taurus(cattle)]
+  * hs1           [Human T2T-CHM13]
+  * hs1_chrR      [Human T2T-CHM13 + chrR rDNA unit]
 
 aspen calls peaks using the following tools:
 
  * MACS2
  * Genrich        [RECOMMENDED FOR USE]
 
 USAGE:
-  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.2.0/aspen -w/--workdir=<WORKDIR> -m/--runmode=<RUNMODE>
+  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w/--workdir=<WORKDIR> -m/--runmode=<RUNMODE>
 
 Required Arguments:
 1.  WORKDIR     : [Type: String]: Absolute or relative path to the output folder with write permissions.
@@ -72,18 +78,18 @@ Optional Arguments:
 --help|-h       : print this help
 
 Example commands:
-  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.2.0/aspen -w=/my/output/folder -m=init
-  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.2.0/aspen -w=/my/output/folder -m=dryrun
-  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.2.0/aspen -w=/my/output/folder -m=run
+  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=init
+  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=dryrun
+  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=run
 
 ##########################################################################################
 
 VersionInfo:
   python          : python/3.10
   snakemake       : snakemake
-  pipeline_home   : /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.2.0
-  git commit/tag  : 4ab396420595c4ccf15416a4c11b523b2d0db862    v1.2.0
-  aspen_version   : v1.2.0
+  pipeline_home   : /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0
+  git commit/tag  : 8d197d39927be3f60558911bd8b2756f36835deb    v1.3.0
+  aspen_version   : v1.3.0
 
 ##########################################################################################
 ```

VERSION

@@ -1 +1 @@
-1.3.0-dev
+1.4.0-dev