build: upgrade tool versions

[uniqueg]

Is your feature request related to a problem? Please describe.

Salmon currently prints the following message to STDERR:

Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###

The Salmon version currently used in ZARP is 1.4.0 - the latest available version is 1.10.1.

Furthermore, #152 seems to have arisen spontaneously and seems to be fixed by upgrading Cutadapt (#153).

These observations highlight that the versions of the tools we use in ZARP are becoming outdated. It might be good to upgrade the tools to the latest versions available on Bioconda before publishing the ZARP manuscript.

Describe the solution you'd like

Upgrade the (Bio)Conda and Docker image versions of all tools to a more recent minor version. Do not upgrade major versions, unless it was verified that any changes to a tool's API do not have an impact on ZARP wiring.

Describe alternatives you've considered

N/A

Additional context

N/A

[uniqueg]

Tracking versions here:

Tool	Current Docker image	Current Conda version	Latest Conda version	Latest GitHub version	Need upgrade?	Comment
ALFA	biocontainers/alfa:1.1.1--pyh5e36f6f_0	1.1.1	1.1.1	1.1.1	No	N/A
BEDTools	biocontainers/bedtools:2.27.1--h9a82719_5	2.27.1	2.31.1	2.31.1	Yes	N/A
Cutadapt	biocontainers/cutadapt:3.4--py37h73a75cf_1	3.4	4.6	4.6	#153	N/A
FastQC	biocontainers/fastqc:0.11.9--hdfd78af_1	0.11.9	0.12.1	0.12.1	Yes	N/A
gffread	biocontainers/gffread:0.12.1--h2e03b76_1	0.12.1	0.12.7	0.12.7	Yes	N/A
HTSinfer	zavolab/htsinfer:latest	0.9.0	0.9.0	0.9.0	Yes (see comment)	now available on BioContainers (replace image and pin version)
kallisto	biocontainers/kallisto:0.46.2--h60f4f9f_2	0.46.2	0.50.1	0.50.1	Yes	N/A
pigz	bytesco/pigz	2.6	2.8	2.8	Yes	Docker image version not pinned; not from BioContainers
r-merge-kallisto	biocontainers/r-merge-kallisto:0.6--hdfd78af_0`	0.6	0.6	0.6	No	N/A
Salmon	biocontainers/salmon:1.4.0--h84f40af_1	1.4.0	1.10.2	1.10.2	Yes	N/A
SAMtools	biocontainers/samtools:1.3.1--h1b8c3c0_8	1.9	1.19.2	1.19.2	Yes	N/A
sra-tools	ncbi/sra-tools	2.11.0	3.0.10	3.0.10 (2.11.3)	Yes (see comment)	Available on Bioconda, so BioContainers image should be available (replace image and pin version); try major version bump first
STAR	biocontainers/star:2.7.8a--h9ee0642_1	2.7.8a	2.7.11b	2.7.11b	Yes	N/A
tin-score-calculation	biocontainers/tin-score-calculation:0.6.3--pyh5e36f6f_0	0.6.3	0.6.3	0.6.3	No	N/A
ucsc-bedgraphtobigwig	biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2	377	455	N/A	Yes	N/A
MultiQC & plugins	biocontainers/zavolan-multiqc-plugins:1.3--pyh5e36f6f_0	1.10.1 / zavolan-multiqc-plugins: 1.3	1.19 / 1.3	1.9 / 1.3	No	Upgrading MultiQC would require a new plugin release; given that we haven't received any bug reports from MultiQC, it's probably not worth it at this point
zgtf	biocontainers/zgtf:0.1.1--pyh5e36f6f_0	0.1.1	0.1.2	0.1.2	Yes	N/A
zpca	biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0	0.8.3.post1	0.8.3.post1	v0.8.3-1	No	N/A