Add 'local profile (#108)

* feat: add a 'profile/local' profile that does not run with a cluster

* feat: parse the snakemake `config` object into a type-hinted dataclass

* feat: add directory options for benchmarks and logs

* feat: create enter/exit dunder methods for `NCBI` class

* feat: download cdna fasta file for salmon

* refactor: use `with Path(...).open()` to open files for I/O

* feat: add `--log` cli option; write logs to file if provided

* feat: create environments for gffread and salmon

* feat: update fastq-screen to 0.16.0

* refactor: do not require httpx for rich for STAR environment

Author: JoshLoecker

envs/gffread.yaml

@@ -0,0 +1,4 @@
+channels:
+  - bioconda
+dependencies:
+  - gffread=0.12.7

envs/salmon.yaml

@@ -0,0 +1,4 @@
+channels:
+  - bioconda
+dependencies:
+  - salmon=1.10.3

envs/screen.yaml

@@ -1,5 +1,5 @@
 channels:
   - bioconda
 dependencies:
-  - fastq-screen=0.14.0
+  - fastq-screen=0.16.0
   - bowtie2=2.4.4

envs/star.yaml

@@ -2,5 +2,3 @@ channels:
   - bioconda
 dependencies:
   - star=2.7.9a
-  - httpx<1.0.0
-  - rich<14.0.0