removed static reports folder

FROM nfcore/base:1.14

LABEL authors="chris.cheshire@crick.ac.uk" \

        description="Docker image containing all requirements for development of static reports"

# Install conda packages

COPY ./environment.yml /

RUN conda env create -f /environment.yml && conda clean -a

ENV PATH /opt/conda/envs/reporting/bin:$PATH

#!/bin/bash

docker build -f dev/docker/static_reports/Dockerfile -t luslab/cutandrun-dev-reporting:latest dev/docker/static_reports

# conda env create -f environment.yml

name: reporting

channels:

  - conda-forge

  - bioconda

  - defaults

dependencies:

  # python version

  - python=3.8.3

  # conda packages

  - numpy=1.20.*

  - pandas=1.2.*

  - seaborn=0.11.*

  - pyranges=0.0.96

  - pysam=0.16.0.1

#!/bin/bash

docker run --rm -v "$PWD":/home/repo -it luslab/cutandrun-dev-reporting:latest /home/repo/bin/reporting.py gen_reports \

--meta /home/repo/results/04_reporting/meta_table.csv \

--raw_frag /home/repo/results/03_peak_calling/06_fragments/*frag_len.txt \

--bin_frag /home/repo/results/03_peak_calling/06_fragments/*bin500*.bed \

--seacr_bed /home/repo/results/03_peak_calling/04_called_peaks/*bed.*.bed \

--bams /home/repo/results/02_alignment/bowtie2/target/markdup/*.bam \

--output /home/repo/dev/docker/static_reports/test_output \

--log /home/repo/dev/docker/static_reports/test_output/log.txt

#!/bin/bash

bin/reporting.py gen_reports \

--meta "results/04_reporting/meta_table.csv" \

--raw_frag "results/03_peak_calling/06_fragments/*frag_len.txt" \

--bin_frag "results/03_peak_calling/06_fragments/*bin500*.bed" \

--seacr_bed "results/03_peak_calling/04_called_peaks/*bed.*.bed" \

--bams "results/02_alignment/bowtie2/target/markdup/*.bam" \

--output "dev/docker/static_reports/test_output" \

--log "dev/docker/static_reports/test_output/log.txt"