#Routine pipelines with dockers/singularity images
1.RNA-seq: https://rumball.readthedocs.io/en/latest/
2.ChIP-seq: https://churros.readthedocs.io/en/latest/
3.Hi-C: https://custardpy.readthedocs.io/en/latest/
4.Single-cell: https://github.com/rnakato/ShortCake
Tip 1: change the sif image into sandbox so that we can edit the sif image
singularity build --sandbox /path/to/rumball_sandbox /path/to/rumball.0.7.4.sif
singularity shell --writable /path/to/rumball_sandbox # now we enter the sif image and we can do some modifications as we need
singularity exec /path/to/rumball_sandbox /opt/RumBall/rsem_merge_GeneOnly.sh "$HaCaT_WT $HaCaT_C3KO" Matrix_deseq2/HaCaT_WT_C3KO $Ddir # rsem_merge_GeneOnly.sh is the modified script inside the sif image
#Single-cell genomics (very comprehensive)
https://www.sc-best-practices.org/preamble.html