need to align .sh calls with new arg counts

[lthealy]

When adding subtypes, I also dropped a never used argument. I will put in a PR that homogenizes and reference this issue. Docker version in #18 works with proposed PR (ran locally using run-v1.sh with updated til_align repo) but will likely have one more rebuild of the image due to an updated main branch

[lthealy]

Current:

        --entrypoint Rscript \
        "$tilalign_container" \
            --vanilla \
            /code/commandLineAlign.R \
            inceptionv4 \
            "/data/results-tils" \
            0.1 \
            "/data/results-tumor" \
            0.5 \
            "" \
            output.csv \
            "/data/results-tilalign" \
            true \
            "/data/sample_info.csv"

New:

 --entrypoint Rscript \
        "$tilalign_container" \
            --vanilla \
            /code/commandLineAlign.R \
            inceptionv4 \
            "/data/results-tils" \
            0.1 \
            "/data/results-tumor" \
            0.5 \
            "/data/sample_info.csv" \ <- this gets moved up from last, and the blank one gets deleted
            output.csv \
            "/data/results-tilalign" \
            true \
            true <- this needs to be the "contains subtypes" toggle argument (Catches any version of TRUE,true,t,T,"true")