vari-bbc · wenjie1991 · Apr 14, 2026 · Apr 27, 2026 · Apr 27, 2026
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,10 @@
+index_files/*.csv
+index_files/*.xlsx
+raw_data/*.gz
+.nextflow/*
+.nextflow.log*
+work/*
+results/*
 bk/
 .nextflow/
 .nextflow.log*

diff --git a/METHODS.md b/METHODS.md
@@ -24,8 +24,6 @@ The merged workflow supports two input modes:
 - `src/rewrite_fastq_barcodes.cpp`: fast C++ implementation for barcode rewriting.
 - `tools/build_rewrite_fastq_barcodes.sh`: build script for the C++ binary.
 - `envs/cuttag-preprocess.yml`: Conda environment for all required tools.
-- `containers/cuttag-preprocess.sif`: default Singularity/Apptainer image path used by the config.
-- `containers/cuttag-preprocess.def`: definition file used to build the Singularity/Apptainer image.
 
 ## Required software
 
@@ -44,30 +42,6 @@ For faster barcode rewriting, build the compiled helper once:
 
 The wrapper used by Nextflow prefers the compiled binary and falls back to Python only if the binary is unavailable.
 
-If you use `singularity` or `apptainer`, the default image path is `containers/cuttag-preprocess.sif`.
-
-You can build that image from the repository with:
-
-```bash
-containers/build_singularity_image.sh
-```
-
-or manually on a local Linux machine with root or sudo privileges:
-
-```bash
-sudo singularity build containers/cuttag-preprocess.sif containers/cuttag-preprocess.def
-```
-
-That image should contain:
-
-- `python3`
-- `cutadapt`
-- `bowtie2`
-- `samtools`
-- `bedtools`
-- `bgzip`
-- `bedGraphToBigWig`
-
 ## Required inputs
 
 - `--input_mode`: `paired_fastq` or `demux`.
@@ -184,29 +158,6 @@ nextflow run main.nf -profile slurm,conda \
   --out_dir results
 ```
 
-Run with Singularity or Apptainer:
-
-```bash
-nextflow run main.nf -profile singularity \
-  --input_dir /path/to/fastq \
-  --barcode_matrix /path/to/barcode_matrix.csv \
-  --ref /path/to/bowtie2/index_basename \
-  --chrom_sizes /path/to/genome.chrom.sizes \
-  --out_dir results
-```
-
-Override the default Singularity image location if needed:
-
-```bash
-nextflow run main.nf -profile singularity \
-  --singularity_image /path/to/container.sif \
-  --input_dir /path/to/fastq \
-  --barcode_matrix /path/to/barcode_matrix.csv \
-  --ref /path/to/bowtie2/index_basename \
-  --chrom_sizes /path/to/genome.chrom.sizes \
-  --out_dir results
-```
-
 ## Notes
 
 - The pipeline keeps the same adapter sequence and Bowtie2 arguments used in the existing shell script.
@@ -216,6 +167,4 @@ nextflow run main.nf -profile singularity \
 - The barcode rewrite step is a required part of the workflow and prefers a compiled C++ implementation for speed, while preserving the original Python code as a fallback.
 - The alignment step preserves the original high-memory setting (`256 GB`, `16 CPUs`, `18h`) but these can be changed in `nextflow.config`.
 - Intermediate files are published into subdirectories under `--out_dir`.
-- The Singularity and Apptainer profiles use `containers/cuttag-preprocess.sif` by default and can be overridden with `--singularity_image`.
-- The Singularity and Apptainer profiles bind `./data` from the Nextflow launch directory by default. Override with `--container_bind_paths` if references or data are stored elsewhere.
 - Sample-name filtering is configurable through `--enable_sample_filter` and `--skip_patterns`, but no samples are excluded unless patterns are provided explicitly.
diff --git a/README.md b/README.md
@@ -20,16 +20,13 @@ The pipeline covers:
 ## Main Files
 
 - `main.nf`: main Nextflow workflow
-- `nextflow.config`: runtime profiles and resource defaults
+- `nextflow.config.temp`: template runtime profiles and resource defaults, please copy to `nextflow.config` and edit as needed
 - `bin/rewrite_fastq_barcodes`: wrapper that prefers the compiled barcode-rewrite binary
 - `bin/rewrite_fastq_barcodes.py`: barcode rewrite helper extracted from the notebook
 - `bin/modify_scict_header.sh`: generic header normalizer used for sciCT demultiplexing mode
 - `src/rewrite_fastq_barcodes.cpp`: fast C++ implementation of barcode rewriting
 - `tools/build_rewrite_fastq_barcodes.sh`: build script for the C++ binary
 - `envs/cuttag-preprocess.yml`: Conda environment definition
-- `envs/cuttag-preprocess-container.yml`: lighter Conda environment used inside the Singularity/Apptainer image
-- `containers/cuttag-preprocess.def`: Singularity/Apptainer definition file
-- `containers/cuttag-preprocess.sif`: default Singularity image path expected by the config
 - `METHODS.md`: extended workflow notes and examples
 
 ## Faster Barcode Rewriting
@@ -183,79 +180,6 @@ nextflow run main.nf -profile slurm,conda \
   --out_dir results
 ```
 
-### Singularity / Apptainer
-
-Build the image from the included definition file:
-
-```bash
-containers/build_singularity_image.sh
-```
-
-On a local Linux machine where you have sudo privileges, the helper runs:
-
-```bash
-sudo singularity build containers/cuttag-preprocess.sif containers/cuttag-preprocess.def
-```
-
-If you use Apptainer instead:
-
-```bash
-sudo apptainer build containers/cuttag-preprocess.sif containers/cuttag-preprocess.def
-```
-
-If you cannot build locally, use a remote builder or ask your HPC admins to build it:
-
-```bash
-singularity build --remote containers/cuttag-preprocess.sif containers/cuttag-preprocess.def
-```
-
-Equivalent helper command:
-
-```bash
-containers/build_singularity_image.sh remote
-```
-
-Then run:
-
-```bash
-nextflow run main.nf -profile singularity \
-  --input_dir /path/to/fastq \
-  --barcode_matrix /path/to/barcode_matrix.csv \
-  --ref /path/to/bowtie2/index_basename \
-  --chrom_sizes /path/to/genome.chrom.sizes \
-  --out_dir results
-```
-
-To use a different image location:
-
-```bash
-nextflow run main.nf -profile singularity \
-  --singularity_image /path/to/container.sif \
-  --input_dir /path/to/fastq \
-  --barcode_matrix /path/to/barcode_matrix.csv \
-  --ref /path/to/bowtie2/index_basename \
-  --chrom_sizes /path/to/genome.chrom.sizes \
-  --out_dir results
-```
-
-If your references or data are outside the working directory, bind those filesystem roots into the container. The default bind path is `./data` relative to the directory where you launch Nextflow.
-
-```bash
-nextflow run main.nf -profile singularity \
-  --container_bind_paths ./data \
-  --input_dir /path/to/fastq \
-  --barcode_matrix /path/to/barcode_matrix.csv \
-  --ref /varidata/research/projects/bbc/versioned_references/latest/data/hg38_gencode/indexes/bowtie2/hg38_gencode \
-  --chrom_sizes /varidata/research/projects/bbc/versioned_references/2024-10-31_10.56.03_v17/data/hg38_gencode/sequence/hg38_gencode.fa.fai \
-  --out_dir results
-```
-
-For multiple roots, provide a comma-separated list:
-
-```bash
---container_bind_paths ./data,/scratch,/home
-```
-
 ## Defaults
 
 - sample-name filtering is available but no filename patterns are excluded unless `--skip_patterns` is provided
@@ -269,6 +193,4 @@ For multiple roots, provide a comma-separated list:
 
 - `nextflow` must be installed on the host system.
 - The Conda profile creates the software environment automatically from `envs/cuttag-preprocess.yml`.
-- The Singularity and Apptainer profiles use `containers/cuttag-preprocess.sif` by default.
-- Singularity and Apptainer bind `./data` from the launch directory by default; override with `--container_bind_paths` if needed.
 - Sample filtering is controlled by `--enable_sample_filter` and `--skip_patterns`.
diff --git a/containers/README.md b/containers/README.md
diff --git a/containers/build_singularity_image.sh b/containers/build_singularity_image.sh
diff --git a/containers/cuttag-preprocess.def b/containers/cuttag-preprocess.def
diff --git a/method.txt b/method.txt
diff --git a/nextflow.config → nextflow.config.temp b/nextflow.config → nextflow.config.temp
@@ -1,6 +1,5 @@
 manifest {
     name = 'cocnt-cuttag-preprocess'
-    author = 'OpenAI Codex'
     homePage = '.'
     description = 'Nextflow pipeline for CoCnT/CUT&Tag barcode rewriting, trimming, alignment, BED, and BigWig generation.'
     version = '0.1.0'
@@ -30,10 +29,6 @@ params {
     chrom_sizes = null
     publish_mode = 'copy'
     conda_env = "${projectDir}/envs/cuttag-preprocess.yml"
-    singularity_image = "${projectDir}/containers/cuttag-preprocess.sif"
-    // Bind the launch directory's data/ tree by default so local references,
-    // annotations, and test assets are visible inside Singularity/Apptainer.
-    container_bind_paths = "${launchDir}/data"
 }
 
 process {
@@ -69,30 +64,11 @@ profiles {
 
     slurm {
         process.executor = 'slurm'
-        singularity.enabled = false
         conda.enabled = false
     }
 
     conda {
         conda.enabled = true
         process.conda = params.conda_env
     }
-
-    singularity {
-        singularity.enabled = true
-        apptainer.enabled = false
-        singularity.autoMounts = true
-        // Additional roots can be supplied with --container_bind_paths.
-        singularity.runOptions = "--bind ${params.container_bind_paths}"
-        process.container = params.singularity_image
-    }
-
-    apptainer {
-        apptainer.enabled = true
-        singularity.enabled = false
-        apptainer.autoMounts = true
-        // Additional roots can be supplied with --container_bind_paths.
-        apptainer.runOptions = "--bind ${params.container_bind_paths}"
-        process.container = params.singularity_image
-    }
 }