also md5sum symlinks

[henningonsbring]

Background

We link fastq files into jobs instead of moving them

Problem/Issue

The current md5sum generation won't generate md5sums for symlinks

What have I done

Added a command that supports symlinks for md5sum generation

Check list

I have:

• Tested with Stub run
• Tested on our HPC

[henningonsbring]

The find command find links:

find . -type l
./fastq/A_control_S1_L001_R1_001.fastq.gz
./fastq/A_control_S1_L001_R2_001.fastq.gz

The command was ran standing in this folder:

tree ../9999_999/
../9999_999/
├── crap
│   ├── hej.txt
│   └── lol.txt
└── fastq
    ├── A_control_S1_L001_R1_001.fastq.gz -> /projects/fs1/stage_shared/demultiplexed/221111_VH00947_17_AACGHWHM5/2022_179/A_control_S1_L001_R1_001.fastq.gz
    └── A_control_S1_L001_R2_001.fastq.gz -> /projects/fs1/stage_shared/demultiplexed/221111_VH00947_17_AACGHWHM5/2022_179/A_control_S1_L001_R2_001.fastq.gz

2 directories, 4 files