Use bioconda docker images for widely used public tools

Use bioconda docker images for widely used tools.

Images to be replaced in the Snakefile:

• bedtools:2.27
• bedgraphtobigwig:4
• cutadapt:1.16
• kallisto:0.46.1
• alfa:1.1.1
• fastqc:0.11.9
• samtools:1.10
• bash:5.0.16
• star:2.7.3a
• salmon:1.1.0
• gffread:0.11.7

changed milestone to %pipeline

added To Do pipeline labels

mentioned in issue #143 (closed)

added Doing label and removed To Do label

assigned to @gypas

marked the checklist item bedtools:2.27 as completed

marked the checklist item bedgraphtobigwig:4 as completed

marked the checklist item cutadapt:1.16 as completed

marked the checklist item kallisto:0.46.1 as completed

marked the checklist item fastqc:0.11.9 as completed

marked the checklist item samtools:1.10 as completed

marked the checklist item star:2.7.3a as completed

marked the checklist item salmon:1.1.0 as completed

marked the checklist item gffread:0.11.7 as completed

marked the checklist item fastqc:0.11.9 as incomplete

mentioned in commit 1fe8ac3d

• bedtools: quay.io/biocontainers/bedtools:2.27.1--h9a82719_5
• bedgraphtobigwig: quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2
• cutadapt: quay.io/biocontainers/cutadapt:1.16--py35_2
• kallisto: quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0
• samtools: quay.io/biocontainers/samtools:1.10--h2e538c0_3
• star: quay.io/biocontainers/star:2.7.3a--0
• salmon: quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0
• gffread: quay.io/biocontainers/gffread:0.11.7--h8b12597_0

mentioned in merge request !84 (merged)

marked the checklist item bash:5.0.16 as completed

• bash: docker://ubuntu:focal-20210416